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What is the structure of Chromatin?
Think "Bead of Strings" DNA exists in the condensesd chromatin form in order to fit into the nucleus.  Negatively charged DNA loops twice around positively charged histone octamers to form a nucleosome bead.  Octamer histones consist primarily of Lysine and Arginine amino acids (positively charged).
What Histone parts are in the Octamer, and what Histone parts are outide thie nucleosome core?
2 sets of H2A, H2B, H3 and H4 make up a histone core for a single nucleosome 1 Histone H1 ties the nucleosome bead together in a string pattern.
What is heterchromatin?
Heterochromatin is condensed, transcriptionally intactive, stericealy inaccessible DNA (HeteroChromatin=Highly Condensed)
What are the purines?
Purines are A, G.  Think PUR As Gold (purines)
What are the pyrimidines?
they are C, T, U-Think CUT the PY (pie) Pyrimidines.
Some specifics about? Guanine, Thymine, and Cytosine?
Guanine has a Ketone, Thymine has a methyl, Deamination of cytosine makes Uracil.
What amino Acids are necessary to make purines?
Glycine, Aspartate, and Glutamate-GAG
What is the precursor for all of the Purines..not the amino acids? What about Pyrimidines?
IMP Pyrimidines are from orotate with PRPP added later
What 2 pathways is Carbamoyl phosphate involved with? What is the defect associated with this?
-De novo pyrimidine synthesis and the urea cycle. -Ornithine Transcarbamoylase deficiency (urea cycle) leads to an accumulation of carbamoyl phosphate which is then converted to orotic acid then to pyrimidines.
Whta pathway of pyrimidine synthesis is THF MTHF and DHFR used?
The last portion of the pathway, in the conversion of dUMP to dTMP requiring thymidylate synthase.
Blockage of DHFR stops what pyrimidine process? What drugs block this process?
the conversion of dUMP to dTMP, this blocks thymidylate synthase indirectly and is good for cancer tx. Methotrexate inhibits DHFR Trimethoprin blocks bacterial DHFR 5-FU directly blocks thymidylate synthase.
What does Hydroxyurea block?
Inhibits ribonucleotide reductase, has been found somewhat useful in severe cases of sickle cell.
What is Orotic Aciduria? What findings do you see? what is the treatment?
It is the inability to convert orotic acid to UMP (in the de novo pyrimidine syntehsis pathway) due to a defect in either the orotic acid phosphoribosyltransferase or orotidine 5'-phosphate decarboxylase, it is Autosomal Recessive. Findings: Orotic aciduria, megaloblastic anemia (without improvement with b12 or folate administration) failure to thrive, NO HYPERAMMONEMIA-(as is seen in OTC  deficiency) Tx, oral uridine administration.
What are the 4 enzymes found in the purine salvage pathway and what does each one do?
1) HGPRT and PRPP- Guanosine to GMP, hypoxanthine to IMP 2) APRT and PRPP- Adenine to AMP 3) Adenosine deaminase-Adenosine to Inosine, for recovery from hypoxanthine 4) Xanthine oxidase (xanthine to uric acid)
An Adenosine Deaminase deficiency causes what disorder?
It can cause SCID (a major cause)-due to excess ATP and dATP imbalances nucleotide pool via feedback inhibition of ribonucleotide reductase, this prevents DNA synthesis and thus lowers lymphocyte count.   
A patient comes in with self mutilation, retardation, aggression, hyperuricemia, gouty tophi, and choreoathetosis?
HGPRT deficiency-Lesch Nyhan syndrome-defective purine salvage makes a lack of hypoxanthine conversion to IMP, Guanine and GMP, so it goes the otherway to form xanthine, then uric acid.
What are the four main features of the genetic code?
1) Unambiguous-each codon is only for 1 amino acid. 2) Degenerate/redundant-More than 1 codon may code for the same amino acid 3) Commaless, nonoverallapping-read from a fixed starting point as a continoud sequence of bases. 4) Universal-Genetic code is conserved throughout evolution.
What are the 4 types of mutations that can occur in DNA and the effects they cause?
1) Silent-same a.a., often base change in the 3rd position wobble. 2) missense-Change a.a. (conservative-new a.a. is similar in structure) 3) Non-sense-Change resulting in an early stop codon 4) Frame Shift-Change resulting in misreading of all nucleotides downstream, usually resulting in a TRUNCATED, NONFUNCTIONAL protein. Severeity is nonsense>missense>silent
DNA terms: Origin of Replication?
  • First, the origin DNA is bound by the Origin Recognition Complex (ORC) which, with help from two further protein factors (Cdc6 and Cdt1), load the Mini Chromosome Maintenance (or MCM) protein complex.
  • Once assembled, this complex of proteins indicates that the replication origin is ready for activation. Once the replication origin is activated, the cell's DNA will be replicated
Replication fork?
Y-shaped region along the DNA template where the leading strand and lagging strand are synthesized.  Compose of the replisome proteins. DNA Helicase:DNA Helicase also known as helix destabilizing enzyme Unwinds the DNA double helix at the Replication Fork. DNA Polymerase III: Builds a new duplex DNA strand by adding nucleotides in the 5' to 3' direction. Also performs proof-reading and error correction. DNA clamp: A protein which prevents DNA polymerase III from dissociating from the DNA parent strand. Single Stranded Binding Proteins (SSBPs):SSBs are the proteins that bind to ssDNA and prevent the DNA double helix from re-annealing after DNA helicase unwinds it thus maintaining the strand separation. Topoisomerase: Relaxes the DNA from its super-coiled nature. DNA Gyrase: Relieves strain of unwinding by DNA helicase. DNA Ligase: Re-anneals the semi-conservative strands and joins Okazaki Fragments of the lagging strand. Primase: Provides a starting point of RNA (or DNA) for DNA polymerase to begin synthesis of the new DNA strand.
What do single stranded binding proteins do?
They prevent the single strands from re-annealing to either counterpart DNA or to free floating nucleotides.
What do DNA topoisomerases do?
They create a nick in the helix to relieve supercoils created during replicatoin-Humans have type 1 and type 2 topoisomerases. Type I topoisomerase cuts one strand of a DNA double helix, relaxation occurs, and then the cut strand is reannealed. Cutting one strand allows the part of the molecule on one side of the cut to rotate around the uncut strand, thereby reducing stress from too much or too little twist in the helix. Such stress is introduced when the DNA strand is "supercoiled" or uncoiled to or from higher orders of coiling. Type II topoisomerase cuts both strands of one DNA double helix, passes another unbroken DNA helix through it, and then reanneals the cut strand. It is also split into two subclasses: type IIA and type IIB topoisomerases, which share similar structure and mechanisms. Examples of type IIA topoisomerases include eukaryotic topo II, E. coli gyrase, and E. coli topo IV. Examples of type IIB topoisomerase include topo VI. Type II topisomerases utilize ATP hydrolysis.
DNA Primase?
Makes an RNA primer on which DNA polymerase III can initiate replication.
DNA polymerase III?
Prokaryotic only, Elongates leading strand by adding deoxynucleotides to the 3' end. Elongates lagging strand until it reaches primer of preceding fragment. 3'-5' exonuclease activity "proofreads" each added nucleotide. DNA polymerase III has 5'-3' synthesis with a 3'-5' proofrooding exonuclease.
DNA polymerase I?
Prokaryotic only, degreates RNA primer and fills in the gap with DNA.
DNA ligase?
Seals the newly formed DNA.
What does DNA polymerase Delta do?
DNA polymerase delta is an enzyme complex found in eukaryotes that is involved in DNA replication and repair, and it consists of the proliferating cell nuclear antigen (PCNA), the multisubunit replication factor C, and the 4 subunit polymerase complex
What is the PCNA?
PCNA stands for proliferating cell nuclear antigen.  It is also known as the DNA polymerase Delta clamp.  IT is an integral part of the replicasome.
What disease is found in a person who has a nucleotide excision repair defect?
Xeroderma pigmentosa-dry skin-with melanoma and other cancers, defect in fixing thymidine dimers. Nucleotide excision repair-specific endonucleases that release the oligonucleotide-containing damaged bases: DNA polymerase and ligase fill and reseal the gap, respectively.
What occurs in base excision repair?
Specific glycosylases recognize and remove damaged bases, AP endonuclease cuts DNA at apyrimidinic site, empty sugar is removed and the gap is filled and resealed.
Mismatch repair?
Unmethylated, newly synthesized string is recognized, mismatched nucleotides are removed, and the gap is filled and resealed. Disease in this pathway is HNPCC.
What is non-homologous end joining?
When 2 ends of DNA fragments are brought together, it isn't required for homology.
Drugs that block DNA replication have what?
They have a modified 3' OH group that causes chain termination. This is due to the 5'-3' direction of DNA synthesis.
What are the three types of RNA, and the types of RNA polymerase?
rRNA, mRNA and tRNA- Think Rampant Massive and Tiny Type 1 RNA polymerase (rRNA), type 2 (mRNA), type 3 (tRNA)-Ross Man Tits.
What is the start and stop codons? In Eukaryotes and Prokaryotes?
Start is AUG (rarely GUG)-AUG inAUGarates protein synthesis. In Euk-codes for methionine, which may be removed before translation is completed. in Pro-codes for Formyl-methionine STop codons-UGA,UAA,UAG
What is the order from 5' to 3' of the functional organization of a gene?
5'-promotor-enhancer-promotor-TATA-transcription initiation site-Coding region (exons and introns)-AATAAA-3'
What is the job of the Promotor? The Enhancer? Silencer?
The promotor is a site where RNA polymerase and multiple other transcription factors bind to the DNA upstream from the gene locus.  (AT-rich upstream sequence with TATA and CAAT boxes)-Promotor mutation commonly results in dramatic decrease in the amount of gene transcribed. -The enhancer is a stretch of DNA that alters gene expression by binding transcription factors -The silencer-is a site where negative regulators (repressors) bind Both the enhancer and the silencer sites may be located close, within, or far away from the gene who's expression is being regulated.
What does Alpha Amantin do?
It inhibits RNA polymerase II, causing a fairly abrupt liver failure.
RNA polymerase in prokaryotes?
1 RNA polymerase is a multisubunit complex that makes all 3 types of RNA.
Explain the process of RNA processing in eukaryotes after transcription?
1) Capping on 5' end (usually a 7-mehtylguanosine) 2)Polyadenylation-aka 3' tail (Poly A tail-100's of A's) 3) Splicing out of introns The RNA is called heterogenous nculear RNA before it is capped and tailed, at which point it is called mRNA.  
What is the signal for the formation of the 3' polyadenylation tail?
AAUAAA And remember that only processed RNA is transported outisde the nucleus.
What are the 3 steps in the splicing out introns?
1) primary transcript combines with snRNP's and other proteins to form the spliceosome 2) Lariat-Shaped (looped) intermediate is generated 3) Lariat is released to remove intron precisely and join 2 exon
What problem with RNA processing does a person with Lupus have?
People with lupus make autoantibodies against the snRNP's so that the splicing out of introns occurs improperly or not at all in certain cells.
Introns vs. Exons?
Introns are intervening sequences and stay in the nucleus.  Exons Exit and are EXpressed. Different exons can be combined by alternative splicing to make unique proteins in different tissues (as in b-thalassemia mutations)
What is the structure or tRNA?
tRNA is a 75-90 nucleotide long, secondary structur in a cloverleaf form wher ethe anticodon is opposite 3' AMINOACYL end.  All tRNA's both euk, and prok. have CCA at the 3' end along with a high percentage of chemically modified bases the amino acid is covalently bound to the 3' end of the tRNA.
What is the process for charging an aminoacyl tRNA?
Aminoacyl-tRNA synthase (1 per a.a. "matchmaker, uses ATP) scrutinizes a.a. before and after it binds to the tRNA if incorrect the bond is hydrolyzed and the a.a. is released and it tries again.  The aa-tRNA bond has energy for formation of a peptide bond.  A MISCHARGED tRNA READS USULAL CODON AN INSERTS WRONG A.A. This process uses 1 ATP-AMP+PPi Tetracycliens bind the 30s Subunit in bacteria and prevent tRNA binding.
What is tRNA wobble?
Accurate base pairing is required only in the first 2 nucleotide positions of an mRNA codon, so codons differeing in the 3rd wobble position may code for the same tRNA amino acid (due to degeneracy of the code)
What are the 3 processes for protein translation?
1-Initiation 2-Elongation 3-Termination
What occurs in Initiation?
Activated by GTP hydrolysis, initiation factors eIF's help assemble the 40S ribosomal subunit with the initiator tRNA and are released when the mRNA and the ribosomal subnit assemble with the complex.
What 3 steps occur during elongation?
1) Aminoacyl-tRNA binds to the A site (except for the initiator methionine) 2)Ribosomal rRNA (aka ribozyme) catalyzes peptide bond formation, transfers growing polypeptide to amino acid in A-site. 3) Ribosome advances 3-nucleotides toward 3' end of the RNA, moving peptidyl RNA to P site (translocation) A-site-incoming AminoAcyl tRNA P-site=accommodates growing Peptide E site=holds Empty tRNA as it Exits
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