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SGU: Nucleic Acids

Biochem: DNA, RNA and their friends

Define the term supercoiling DNA double helix that have additional twists applied to them that have coiled up upon themselves
What is a purine? – heterocyclic compound consisting of pyrimidine fused to a 5 member imidazole ring (adenine and guanine)
What is a Pyrimidine? hererocyclic compounds with nitrogen atoms at positions 1 and 3 of a 6 member ring (thymine, cytosine, uracil)
What is a Deoxyribonucleosides? consist of a nitrogenous base and a deoxyribose sugar (H present at 2’ C)
What is a Ribonucleotide? nitrogenous base (attached to 1’ C by B-N-glycosidic bond), a ribose sugar (OH at 2’ C), and a phosphate group (backbone of DNA, attached to 5’ C) – present in RNA molecules
What is a Deoxyribonucleotide? nitrogenous base, deoxyribose sugar and a phosphate group (present in DNA molecules)
Describe the phosphodiester bond The phosphodiester bond is between the 3’ OH group of the deoxyribose/ribose on the last nucleotide and the 5’-phosphate of the dNTP/NTP precurson – basically it is a bond that connects nucleotides in DNA
What is the function of modification made to tRNA and rRNA for (ie. 4-thiouracil, dihyrdouracil)? enzyme/tRNA recognition, tRNA condon recognition, peptide synthesis by ribosome
What is the difference between a ribose and deoxyribose? ribose: OH on 2'carbon Deoxyribose: -H on 2'carbon
Difference between nucleoside and nucleotide? Nucleoside: nitrogenous base and a ribose/deoxyribose sugar Nucleotide: nitrogenase base, ribose/deoxyribose and a phosphate grp
How do you build DNA or RNA polymers DNA/RNA poly catalyzes the formation of a phosphodiester bond between the 3'OH of deoxyribose/ribose on the last nucleotide and the 5'-phosphate of the dNTP/NTP precursor
What is the ratio of purines to pyrimidines in double stranded DNA? 1:1 (ie. 50% purines and 50% pyrimidines)
What is Chargaff's rule? A=T and C=G
What are the 7 properties of DNA? 1. Two polynuc right handed double helix 2. Antiparallel. 3. sugar-phosphate outside, bases inside 4. bases bound by H-bonds 5. complementary base pairing 6. bases .34nm apart, 10 bases/turn,external diameter is 2nm 7. major and minor groove
How long is each DNA stand/cell? 2 metres
What are the different structural forms of DNA? Z-DNA, B-DNA and A-DNA
Describe Z-DNA left handed helix. may be involved in gene regulation
Describe A-DNA right handed helix, dehydrated state, no biological significance.
In nature how does DNA exist? It exists in tertiary (supercoiling) and quarternary structures (coiling with histones).
What protein is involved in creating supercoiling? topoisomerase
Describe structures and roles of the mRNA linear and single stranded, carries codon information for translation (2%)
Describe structures and roles of the tRNA folded loop structures formed by intra-molecular H-bonding, carries amino acids to ribosomes (16%)
Describe structures and roles of the tRNA linear, single stranded, folded molecule that complexes with protein to form ribosomes (82%)
What is Tm? the temperature at which 50% of DNA becomes single stranded.
What influences Tm? high C-G content (incr Tm), high salt concentration (incr Tm)
What affects the rate of annealing of DNA strands? Size of DNA (long DNA takes longer), complexity of DNA
Describe the function of microRNA? regulate gene expression by binding to a complementary single stranded RNA which triggers the cell to destroy it
Describe FISH. Take a single stranded DNA with gene sequence of interest with a fluorescent probe let it anneal to DNA in cell and look for fluorescence.
How do Nucleoside analog drugs inhibit DNA replication? analogs have a higher affinity for reverse transcriptase and incorporate the analog without an OH grounp on the 3' carbon.
What group does didanosine have in its 3' carbon slot? doesn't have one
What analogs are used for HIV treatment? Didanosine, tenofovir
What analogs are used to kill rapidly dividing cancer cells? Cytosine arabinoside (cytarabine) and Vidarabine (adenosine arabinoside)
How does vidarabine and cytarabine inhibit the activity of DNA poly? 3' OH is in a different planar configuration
What happens to DNA with a lot of methyl groups? DNA transcription is shut of.
What is the purpose of azacytidine and 5-azacytidine? Used to treat cancer by inhibiting methyltransferase enzymes from adding a methyl group to them.
Define supercoiling. Supercoiling compacts DNA; negative supercoiling promotes strand separation while positive supercoiling is introduced during DNA replication and transcription and must be corrected
Which enzymes accomplish DNA coiling in prokaryotes? The topoisomerases: DNA gyrase (topoisomerase II in eukaryotes) and DNA topoisomerase I
What are the functions of supercoiling DNA? 1. Compacts DNA 2.Negative promotes strand separation 3. Positive promotes DNA replication and transciption
Where is positive supercoiling introduced (with respect to the proteins) during DNA replication or transcription? ahead of the protein doing the supercoiling
Where is negative supercoiling introduced (with respect to the proteins) during DNA replication or transcription? behind the protein doing the supercoiling
Which enzymes correct for supercoiling and how? Topoisomerase I: forms a single covalent bond with the DNA and breaks phosphodiester bond to allow free rotation
How does DNA gyrase correct the case of two double helices crossing over each other? 1. makes a covalent linkage to both strands of one helix and making a double stranded break. 2. 2nd DNA is passed through break 3. break is resealed
What is chromatin? complex of DNA and chromosomal proteins (histones)
What is a nucleosome core composed of? H2A, H2B, H3, H4
A nucleosome is connected together by linker DNA and what protein? H1 histone
How does the 30nm fiber form? Interactions between adjacent histone H1 proteins.
Which base pair is methylated during transcriptional repression? cytosine
List the antibiotic drugs that interfere with DNA gyrase The quinalone family of antibiotics, including naladixic acid and ciprofloxacin, work by inhibiting DNA gyrase. A halt in DNA replication results due to positive supercoiling ahead of the replication fork.
Describe the structure of chromatin and histone proteins Histones are rich in lysine and arginine, and as a result carry a positive charge. This makes it easier for negatively charged chromatin to associate.
What is the name of the prokaryotic version of histone protein? HU protein
How do DNA and histones interact with eachother? DNA is negatively charged and histones are positively charged and are therefore attracted to eachother.
Define euchromatin. decondensed and transcriptionally active DNA
Define heterochromatin. condensed and transcriptionally inactive DNA
What is the function of DNA methyltransferase enzyme Methylation of cytosine to 5-methyl-cytosine
Describe the mechanism of DNA transcription repression. Following DNA methylation, methyl cytosine binding proteins bind to the DNA, HDAC binds and removes acetyl groups off of histones giving them a greater positive charge and inducing supercoiling.
What happens to DNA when histones are acetylated. euchromatic - active.
What components are required for synthesis of DNA? 1. All four dNTPs 2. A fragment of DNA template 3. DNA poly 4. Mg2+ 5. primer with 3' OH
In what direction does DNA poly read DNA? 3' to 5'
What nucleotide is acyclovir an anologue of? guanine
Which enzyme converts acyclovir to acyclovir triphosphate and in what organism is it found in? enzyme-thymidine kinase; organism-virus
Explain a tautomeric shift. An unstable shift of cytosine to mimic a thymine. It then gets base paired with A.
Explain the significance of origins of replication. site at which DNA replication occurs in both directions
What is leading strand synthesis? Continual synthesis of DNA. Synthesis proceeds towards replication fork.
What is lagging strand synthesis? DNA primase has to drop down a primer. Synthesis proceeds away from the fork.
What is the function of SSB proteins? prevent re-annealing of DNA and prevent hairpin loops from forming
How are Okazaki fragments joined together? DNA ligase which uses ATP.
What is the function of the Clamp protein? tightly holds the DNA poly onto the template for synthesis of long templates and releases DNA poly when it stalls at a region of dsDNA
What drug inhibits bacterial DNA gyrase? Ciprofloxacin
What is the function of telomerase and what kind of activity does it have? It has reverse transcriptase activity. It has an RNA primer and binds it to the DNA overhang to extend. A primer can then be added so DNA poly can fill in that gap
What are the different types of RNA? mRNA, tRNA, rRNA, snRNA
What is snRNA? combines with certain proteins and is involved in RNA processing and gene regulation in eukaryotes
Describe the major steps of RNA synthesis in prokaryotes 1. RNA polymerase binds -35 & -10 region, DNA molecule is unwound, sigma factor disassociates from core enzyme after 8-9 ribonucleotides have been polymerized 2.RNA polymerase unwinds DNA 3.transcription terminated at termination sequence
List the RNAs that are transcribed by the different types of RNA polymerases RNA polymerase I (5.8S, 18 S, 28S rRNA genes), RNA polymerase II (all protein-coding genes like mRNA and some snRNA), RNA polymerase III (tRNA genes and some snRNA)
Explain how Courmarins and quinolones targets and inhibits specfic components of transcription. inhibit bacterial gyrase, causing positive supercoils and subsequent halt of DNA replication and transcription
Explain how Rifamycin targets and inhibits specfic components of transcription. – antibiotic from strain of streptomyces that inhibits transcription initiation by blocking formation of 1st phosphodiester bond, RNA pol of eukaryotes not affected
Is a nucleoside-monophosphate a nucleotide or nucleoside? Nucleoside
How many charges does a nucleotide mono phosphate have? 2 negative charges
What nucleoside triphosphate is involved in protein biosynthesis? GTP
What nucleoside triphosphate is involved in lipid biosynthesis? CTP
What nucleoside triphosphate is involved in carbohydrate biosynthesis? UTP
What nucleoside triphosphate is involved in signal transduction? GTP
What makes A-type DNA different from B-type? bases are not perpendicular to axis, larger major groove and shallower minor groove.
When is A-type DNA observed? When DNA solution is dehydrates, normally with short DNA, dsRNA and DNA/RNA hybrids
How do you denature DNA? high temp or alkali conditions
What is the melting temperature (Tm)? temp at which half DNA is denatured
What does azidothymidine and didanosine do? block reverse transcriptase/do not have a 3' OH
What does acyclovir and tenofovir do? They have an open chain sugar, acyclovir has a high affinity for viral DNA poly (herpes) and tenofovir has a high affinity for reverse transcriptase
What do the arabinosides do? have a different planar arrangement and block DNA replication by DNA poly
What do the cytidine analogs do? block DNA methylation
What are the differences between Prokaryotic and Eukaryotic mRNA? bacterial mRNA are polycistronic and unmodified at 5' & 3' end
When are the RNA processing proteins transferred to the mRNA? Processing proteins travel with RNA poly II and are transferred after initiation of transcription
What enzymes are involved in capping of mRNA? phosphatase, guanylyl transferase, guanine-7-methyl transferase, 2'-O-methyl transferase.
What is the function of phosphatase? removes phosphate from 5' end of RNA
What is the function of guanylyl transferase? Adds GMP in reverse linkage
What is the function of guanine-7-methyl transferase? Adds a methyl group to the 2'-O position to the secondlast base on the 5'end
What is the function of the methyl guanine cap? helps cell distinguish between different RNA, plays a role in regulation of mRNA processing, transport, and translation
What proteins are involved in the modifying the 3' tail of mRNA? CPSF, CstF and cleavage factors, PAP, PABP
What is the function of CPSF? Binds to polyadenylation signal (AAUAAA)
What is the function of CstF? binds GU-rich element
What is the function of cleavage factors? bind (CA sequence) to cleavage site
What is the function of PAP? Adds 200A to 3' end
What is the function of PABP? binds to tail and assists in directing translation
What are the steps of intron removal? 1. U1 binds 3'GU 2. U2 binds Branch point A 3. U4/6 and U5 bind U1 and U2 3. U4 released 4. 3'GU cleaved and G binds A 5. 3' AG cleaved, Exons ligated, spliceosome disassembles
What causes Systemic Lupus Erythematosis? antibodies to U1 snRNA
What causes beta-thalasemmia? mutations in the beta-globin gene that generate additional splice sites within the mRNA
What causes Limb Girdle Muscular Dystrophy? Mutation in calpain 3 gene that generates a new splice site within the exon 16
What can control alternative RNA splicing? weak splice site sequences, negative/positive control
What does the cytidine deaminase enzyme do? introduces a premature stop codon by alternative splicing into APO-B in intestine to make shorter protein.
What does adenosine deaminase do? Changes A to I in glutamate receptor to change glutamine to arginine in brain
How is protein written by RNA poly and DNA poly? 5' to 3', N terminus to C terminus
Which RNA consitutes for 99.9% of total RNA? mRNA, tRNA & rRNA
What does redundant genetic code mean? several codons code for one amino acid
What does non-overlapping genetic code mean? each codon is read three at a time without overlap
What is an inframe mutation? When entire codons are removed or inserted
What are the three stop codons? UGA, UAG, UAA
What is the start codon? AUG
What is the wobble hypothesis? predicts the base pairing of the 5' anticodon and 3' codon.
Which protein does the anticode IGC carry? alanine
Is inosine a purine or a pyrimadine? purine
what is a a charged tRNA? a tRNA with its amino acid group
What enzyme calatyzes the activation of an amino acid? aminoacyl tRNA synthetase
What drives the formation of a charged tRNA? hydrolysis of pyrophosphate
What are the 5 steps of formation of a polypeptide polymer from an RNA template? 1. Activation of the monomer 2. Initiation 3. Elongation 4. Termination 5. Processing the polymer
In prokaryotes, after methionine is activated how what molecule donates it's carbon to make formylmethionine? N-formyltetrahydrofolate
In prokaryotes, how is the correct start codon recognised? 30S binds to the shine delgarno sequence
What catalyzes the translocation of the mRNA relative to the ribosome? EF-G or EF-2 with GTP
How is the terminal amino acid removed from the ribosome? Release factor allows peptidyl transferase to cleave ester bond between tRNA and amino acid
What are the three differences between prokaryotic and eukaryotic translation? prokaryotic:polycistronic, translation and transcription together, internal AUG sites used
How is protein synthesis affected by streptomycin? Binds to 30S/prevents assemble of ribosome
How is protein synthesis affected by tetracycline? Binds to 70S/prevents access to incoming aminoacyl-tRNA
How is protein synthesis affected by erythromycin? Binds to 70S/Block elongation
How is protein synthesis affected by chloramphenicol? Inhibits peptidyl transferase/blocks elongation
How is protein synthesis affected by cyclohexamide? blocks elongation in eukaryotes
How is protein synthesis affected by puromycin? Blocks elongation after forming a peptide bond chain causing peptide to fall out of ribosome P-site
How is trypsinogen cleaved to trypsin? enteropeptidase
What receptor is a tyrosine kinase? the insulin receptor
Created by: mnoronha
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