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Biochemistry Test 3
Tri 2
| Question | Answer |
|---|---|
| James Watson and Francis Crick | described nature od DNA and molecular biology was born |
| Genome | genetic information in the sequence of DNA, one complete set of information(haploid), DNA is in the nucleaus and in mitochondria |
| Central Dogma | DNA is either REPLICATED into more DNA or is TRANSCRIBED into RNA. RNA is then TRANSLATED into PROTEIN |
| Molecular Biology | includes the molecular nature of genetic material and is how the information in DNA id transmitted(inheritance) or translated(gene expression). |
| Replication | the process by which genetic material is duplicated to allow cell division within a generation and allow genetic information to flow from one generration to the next |
| Transcription | the genetic message in DNA is transferred to RNA by the process of DNA directed RNA synthesis. |
| Reverse Transcription | RNA directed DNA synthesis. |
| Transcription Products | mRNA, tRNA, rRNA |
| Translation | when the genetic message is decoded by translating a linear sequence of AA, also called RNA-directected protein synthesis |
| Structure of DNA | double helix (two polynucleotides), antiparallel (oposite polarity ), nitrogenous bases oriented inwards |
| Structure of DNA 2 | 5' to 3' sugar phosphate backbone, B-form of RNA (hydrated form) has 1 Base Pairs /turn. Major and Minor groove. Entire structure stabalized by h-bonds between bases, base stacking innteractions, sugar phosphate backbone on outside interacting with H2O |
| DNA Replication | introduced by Watson and Crick, model suggested a model for faithful duplication-semiconservative DNA replication. In bacteria the genophore is a single circle. In eukaryotes the chrms are linear and multiple |
| Nucleotides | Monomers of Nucleis Acid synthesis. DNA bases are ATGC (deoxyribose). RNA bases are AUGC (ribose) |
| Polymerization | produces a phosphodiester backbone. 5' phosphate in one end and a 3' OH on the other, Extensions add from 3' OH. The chain grow 5' to 3' |
| Watson-Crick base pairs | A-T(2 H bonds produced) G-C . The aromatic nature of nitrogenous bases produces a flat planar interaction, and allows for van der Waals interactions referred to as a base stacking interaction |
| Denaturation of DNA | The two strands of DNA molecule can be seperated by heating or by additions of acid or base. Unwinding the double helix is called melting and if induced by heating has a Tm. Seperated strands will reassociate or reanneal to form the double helix apon co |
| Antiparallel | the sugar phosphate backbone has sugars running in opposite directions. 5' to 3' is reversed from one side to the other |
| Structure of DNA | B- form of DNA is the most common, and is Hydrated. There are 1 base pairs per turn. The helical nature produces a majr and minor groove, these sites are where we can see the bases of DNA |
| A form DNA | dehydrated |
| B form DNA | hydrated |
| Z form DNA | in stretches of DNA which are G-C rich repeats. Alexander rich proposed. Important in gene expression, forms an upstream tight rregion of DNA important in gene expression |
| DNA vs RNA in Alkali(stongly basic) | In an alkaline solution, DNA will denature and RNA is broken down to SS and broken peices. A DNA-RNA hybrid has a RNA broken down leaving ssDNA, which is useful in the lab |
| DNA RNA interaction | We use U instead of T in RNA |
| Eukaryotic DNA | In the nucleaus, the structure beads on string, there are histone protein interactions, |
| Chromatin Structure | H2A, H2b , H3 and H4 makeup bead. There are two copies of each, with a total of 8. There is also an H1 linker. |
| Homologous Chrms | For examole, Chms #1 has a paternal and maternal part. |
| Homologs | contain same basic data set of information, correspondence in a linear fashoin, potential for minor varients between the loci(alleles) |
| Structure of a gene | Each gene has an upstream promoter region, this is important for letting the cellular apparatus know where to begin the transcription. RNA polymerases recognize this region. A portion of the RNA transcribed is the leader and not translated (mRNA) |
| Ribosome | Prokaryotes =70s (50s =30s). Eukaryotes = 80s (60s + 40s) S= sedimentation rate |
| Retroviruses | retro b/c they take the viral RNA and make a DNA copy. They use enzymes called Reverse Transcriptase and have the ability to integrate into the host chms. LTR (long terminal repeats) are used in the process |
| Central Dogma | DNA is TRANSCRIBED into RNA and then the RNA is TRANSLATED into PROTEIN |
| DNA Polymerase | for replication |
| RNA Polymerase | transcription and translation |
| Replication of DNA | achieved through DNA polymerase. Catalyzes the step by step additions of nucleotides to growing polynucleotide chain. Requires all four dNTP's (AGTC) and Mg+2. All additions are to the 3' OH group |
| Replication of DNA 2 | The two strands must be seperated for replication, thus a replication fork is formed. Elongation of the newly synthesized polynucleotide is always 5' to 3'. The opposite strand serves as a template for which a new base will be incorporated |
| Replication of DNA 3 | DNA ploymerase I was the first polymerase discovered. (ARTHUR KORNBURG). He found them in E. coli. The major function is to repair DNA damage, remove RNA primers. DNA polymerase III of E. coli is the major polymerase for the genophore |
| Replication is bi-directional | JOHN CAIRNS did experiments showing the bi-directional nature of replication in E. coli. He labeled the genophore using 3H Thymine. Thymine only doesinto DNA, he termed what he saw as theta structures |
| Replication proteins | note the following |
| Primosome complex (Prok and Euk) | One component of the complex called PRIMASE synthesizes RNS primer |
| Helicase ( Prok & Euk) | unwinds DNA dbl helix, costs 2 ATP/ nucleotide pair |
| Single Stranded Binding Protein (SSB) (Prok & Euk) | stabalizes ssDNA @ replication fork |
| TopoisomerasesI Prok & Euk) | allows strand to spin around, prevents tension |
| Topoisomerase II (Prok & Euk) | DNA gyrase, imp in gene expression |
| DNA Polymerase I (Prok) | Repairs and removes DNA |
| DNA Polymerase II (Prok) | synthesis of bacteria |
| DNA Ligase (Prok & Euk) | seals end of backbone (covalent link) |
| DNA Ploymerase alpha (Euk) | proof readds, lagging strand synthesis |
| Telomerase (euk) | extends length |
| Polymerase Reaction | Each time a new base is added, DNA polymerase senses the proper fit by the size, and proper Watson-Crick pairing. There must always be enough dNTP and Magnesium |
| Steps in DNA replication | The helicase first unwinds the parental strands, SSB's stabilize the ssDNA, Primosome Complex binds the ssDNA and synthesizes RNA complex. DNA poly III uses RNA Primer, but it requires a 3' OH group to befin the replication |
| Steps in the DNA Replication | The RNA primers are removed from the DNA poly I, the new synthesized DNA fragments are joined by DNA ligase. Topoisomerase I relieves upstream tension and Topoisomerase II resolves concatamers. |
| Bruce Albert's Model | Sliding Trobone model of DNA replication showing the arrangement for replication of the lagging strand. |
| Replication of Linear DNA | telomeres of linear chrms are a problem, there is a mechanism to add to these ends so they do not shorten |
| Telomerase | Function is to lengthen telomeresand prevent erosion of genetic information. When this slows, aging of the cell and cancers are thought to occur. Telomerase carries its own RNA primer to extend the ends of chrms (telemeres) |
| DNA Damage | Any change in normal base sequence is a mutation. Some of these lead to cancerous cells. The carcinogen in cigarettes is Cenzol(alpha)pyrene witha GC base pair in DNA leading to Guanine |
| Excision Repair (Depurination Repair) | repair endonucleases that induce a nick into the backbone. DNA pol I senses the nick and DNA ligase seals the backbone again. |
| Deamination fo cytosine to uracil | no uracil is allowed in DNA, the enzyme Uracil-N-glycosylase ung removes uracil. Repair follows as in Depurination repair |
| Thymine Dimer Repair | This is a big problem. Either a short patch (excision repair) or the enzyme called PHOTOLYASE can undo the cyclobutane ring b/tw intrastrand T dimers. PHOTOLYASE utilizes energy from visible light to do the rrepair, they are found in skin cells |
| Recombination | This is at times when damage is great. SOS repair requires that this occur, this is also happening in meiosis when crossing over observed as chi forms are observed. |
| Recombination STEPS | First One strand is nicked and strand invasion occurs. Then a D-loop nick is formed and is nicked which promotes base pair b/tw homologous regions. Ligation occurs and a HOLIDAY STRUCTURE is seen. Cut at 'a' then reseal or cut at 'b' and reseal. |
| Burkitt's lymphoma | Also known as a Robertsonian translocation..Chrms # 8 ans chrms # 14. |
| Acute Polymphocytic Leukemia | translocation at chrms # 15 and 17 |
| Reverse Transcriptase | making a DNA copy of a RNA molecule, this enzyme 1st seen in retroviruses. |
| Reverse Transcription Rxn | There is 1st a copy of RNA template. Then a DNA-RNA hybrid is formed. The RNA is degraded by ribonuclease and leaves only DNA known as cDNA. The cDNA is synthesized into another strand forming dbls cDNA. |
| Transposons | Found by Barbara McClinttock (Nobel Prize). Noted jumping genes which are direct repeats or long terminal repeats that are involved in a non-homologous pairing event. Multi colored corn |
| Transposons and Transposition rxn | staggard breaks are produced by transposase, and insertion of transposon into recipient DNA. The direct repeats are important b/c they are at both ends. These insertions may interupt genes or change gene expression. May also remain quiet and show later |
| HIV | hass these tranposons and transpositions |
| HIV | a retrotransposon first requires reverse transcriptase to make RNA genome into DNA. Now the DNA is subject to tranposition. The DNA is then inserted into the chrms of infected cells, and each time it divides the viral DNA is replicated also |
| Transcription | Synthesis of RNA |
| Regions of a Gene | Promotor region( -#) closer to 5' end. Start point for transcription is +1, after promoter region. The Coding Region starts with a leader RNA and ends with a trailor RNA. |
| What is a gene? | A segment of DNA that generateds an RNA product, or a protein product. The transcribed region contains the template for RNA synthesis, and begins at the start point (+1). A gene also includes an upstream promoter which regulates the production of the pr |
| Alpha | connect subunits |
| Beta | catalyze RNA Synthase |
| Beta ' | Template binding and association with sigma |
| Sigma | recognition of general promoters |
| Regulation of Transccription | Basis if regulation is the prescence of conserved sequences upstream from the gene to be transcribed. Bacteria hae either a promoter region alone (Constitutive expression) or Promotor/Operator( inducible expression) |
| Prokaryote Model | The initial contact point for RNA polymerase to bind is between -70 and -35. Between -7 and -10 is the TATaat box (Pribnow Box) or the promoter box. Transcription starts at +1. |
| Steps in Transcription | Binding-recognitionof 5' upstream. Initiation-begin RNA synthesis(no primer). Elongation-continue polymer. Termintion-stop RNA synthesis. |
| Binding | RNA holoenzyme binds DNA of promoter. sigma facto ris the important factor in recognition of the 5' end. Holoenzyme binds -35 first, then slides down to the pribnow box (-10) =, unwinds DNA and begins at +1 |
| Initiation | The beginning of RNA synthesis, 5' to 3' . First base is TRIPHOSPHATE. second is joined to 3' OH. Sigma dissosociates after 8-9 nucleotides |
| Elongation | Polymerizarion continues, there is movement of core enzyme, requires enough ATP, CTP, GTP and UTP |
| Termination | There are two types..Hairpin loop (GC loop) followed by AAAA in DNA and UUUU in RNA. Also Rho termination protein |
| Euk Transcription | uses several RNA polymerases. more extensive upstream promoter. Modulation |
| Euk RNA Polymerases | see next |
| Euk RNA Pol I | in nucleolus, produces 35s and 47s preribosomal RNA |
| EUk RNA Pol II | Nucleoplasm ..produces heterogenous nuclear RNA |
| Euk RNa Pol III | Nucleoplasm..produces tRNA and more |
| Variation in Regulation | more upstream DNA involved. Cis elements are needed close and Trans are far away. |
| RNA Pol III | promoters for RNA Pol III are found within the coding exons. |
| Differences in gene expression | Prokaryotes -Operons, constitutive and inducible, coupling transcription /translation. Euk- Monocistronic, Intons/Exons, 3 RNA pol, extensive RNA modification, slower gene expression, T/T seperated |
| Prokaryotes | gene expression optimized to change quickly and adapt to env. changes. RNA produced has a half life(3 sec to a minute) |
| Eukaryotes | gene expression complex, slower, long half life( DAYS TO MONTHS) |
| Amanita phalloides | mushroom that produce a toxin alpha amanitin. Death cap. this toxin blocks RNA Pol III. 40-90% die within a few days. |
| mRNA | Prok-no processing. Euk-primary transcript hnRNA. |
| hnRNA | contians transcript for both exons and introns. |
| spliceosome | cuts out introns and splices exons togetherin frame. made up of small nuclear RNA called U1, U2 etc. an dsmall snRNP's |
| Lariat Processing | A common form of hnRNA processing. Conserved sequence observed at 5' end of exon/intron junction. These tell U RNA where to cut and where to splice |
| 7 methyl G cap | joined to 5' end in an unusual 5' to 5' linkage. Ribose sugars in the end may be methylated too. This structure is resistant to 5' exonucleases and this promotes stability of messsage |
| Poly A Tail | Unusual Structure at 3' end. 40-200 A residues(Adenosine) are added post transcriptionally. Their function is to further stabalize the messaga against 3' exonucleases. It also facilitates exit from the nucleus. |
| mRNA Synthesis | 7 me G Cap first, Poly A tail next, Splicing third, release from nucleus to cytosol |
| RNA processing | Physical and Chemical |
| Physical RNA processing | cleavage and loss of parts of RNA, cleavage and rejoining portions of RNA |
| Chemical RNA processing | additions of nucleatides, modifications of existing nucleotides |
| rRNA | genes found at nucleolus, segmental DNA contains tandem repeats in addition the DNA is amplified. 48% is spacer RNA in transcript, 52% is remainder of 18s rRNA |
| tRNA | Removal of 5' leader seq., cut 3' OH nucleotides off and replace with CCA3'OH, extensive modifications to remaining selective bases, euk have also to splice out introns |
| RNA synthesis inhibitors | by binding DNA or RNA Pol. |
| DNA Binders | Actinomycin D |
| RNA Binders | Rifampin, streptolydigin, Euk alpha amanitin |
| Highly Repetitive DNA | 6-100 pairs, millions of copies, clustered locations, centromers, telomers, 10% of human genome not Transcribed |
| Moderate Repetitive DNA | few to 10000 copies, 25% of human genome, transcribed by rRNA, tRNA histones |
| Translation | protein synthesis, protein is final structure, requires all 3 forms of ribosome and magnesium, potassium |
| Basis of Translation | A gene is usually over 1,000 nucleotides long, the nucleotides are trancribed to RNA. Codons are triplets of nucleotides |
| Genetic Code | based on triplet or codon. The code has a reading frame, and is non-overapping. There are multile codons for the same AA |
| Point Mutation | a single base is changed in the DNA producing a single change in RNA |
| Silent Mutation | do not affect AA seq. |
| Missense Mutation | one AA is replaced by another AA in the protein sequence |
| Nonsense Mutation | premature termination of chain, change from codon to a stop codon |
| Wobble Hypothesis | helps to account for degeneracy of the code. H- bonding at the first and second positions of the codon are normal Watson-Crick pairs. H bonds at the third is flexible- the base Inosine in anticodon can bind with U, A and C |
| GC Characteristics | there is only 1 codon for 2 AA. AUG in mRNA codes for methionine. All proteins start with meth. UGG codes for tryptophan, no other codon. UAA, UAG and UGA are nonsense codons, they stop translation |
| Components of Translation | Amino-acyl-tRNA synthetases, these are enzymes that charge the tRNA with their AA.Requires two high energ P from ATP. forms Amp |
| Energy expediture | energy is used in formation of initiation complex, loading incoming charged tRNA and everthing else |
| Codon Recognotion | via H-bonding to the anticodon of charged tRNA |
| Steps in Translation | Initiation Complex, Elongation, Termination |
| Initiation Complex | 30s ribosomal subunit finds Shine-Dalgarno sequence in the 5' end of mRNA. Initiato tRNA H-bonds with AUG in P site. 50s Ribosomal subunit joins complex |
| Initiation Factors | must be present |
| REVIEW QUESTIONS GIVEN IN CLASS | (blank) |
| Replication | the process by which genetic material is duplicated to allow cell division within a generation and allow genetic information to flow from one generation to the next |
| Transcription | The process when genetic message in DNA is transferred to RNA by the process of DNA DIRECTED RNA SYNTHESIS . The transcription products are mRNA, tRNA, rRNA |
| Reverse Transcription | RNA DIRECTED DNA SYNTHESIS |
| Translation | the genetic message is decoded by translatinf a linear sequence of nucleotides into a linear seq. of AA |
| Watson and Crick | DNA model and semiconservative replication |
| B form DNA | most common, 10 base pairs per turn, major and minor groove(where you can see the nitrogenous basis) |
| Z form DNA | Found by Alexander Rich, stretches of DNA that are GC rich, forms an upstream tight region |
| Sugar Phosphate backbone | found on the outside |
| Gene expression | upstream region |
| Alkali Solution and DNA | DNA denatures |
| Alkali Solution and RNA | RNA breaks down into peices of mononucleotides |
| Chromatin Structure | contains H2A, H2B, H3 and H4. There are 2 of each, and an H1 linking them all |
| Homologous Chrms | contain paternal and maternal parts |
| Prokaryote Ribosomes | 70s (50s+30s) |
| Eukaryote Ribosomes | 80s (60s +40s) |
| Retroviruses | they take viral RNA and make a DNA copy by using enzyme reverse transcriptase. LTR's are used in this process |
| Arthur Kornberg | discovered Polymerase I, found in E. coli cells. Poly III of E. coli is major poly for the genophore |
| John Cairns | showed bidirectional nature of E. coli. Isolated a theta structure |
| REPLICATION PROTEINS | (blank) |
| Primosome Complex (prok and euk) | synthesizes RNA primer |
| Helicase (prok and euk) | unwinds DNA dbl helix, costs 2 ATP |
| SSB (prok and euk) | stabalizes ssDNA at replication fork |
| Topoisomerase I (prok and euk) | allows strand to spin around, prevents tension |
| Topoisomerase II (prok and euk) | DNA gyrase, imp in gene expression, resolves concantamers` |
| DNA Poly I (prok only) | Repairs and removes DNA |
| DNA Poly II (prok only) | synthesizes bacteria |
| DNA Ligase (prok and euk) | seals end of backbone (covalent link) |
| DNA Poly alpha (euk) | proof reads lagging strand |
| DNA Poly sigma (euk) | synthesizes leading strand |
| Telomerase (euk) | extrends length at end |
| S phase | Replication of DNA |
| Bruce Alberts | sliding Trombone model, shows replication of lagging strand |
| Telomerase | (blank) |
| Cigarette Carcinogen | Benzol(alpha)pyrene |
| Excision Repair | repair endonucleases and induce a nikc into backbone, DNA Poly I senses nick, DNA ligase seals backbone |
| Thymine Dimer Repair | same as excision repair. Photolase is backup |
| Reverse Transcriptase Rxn | Copy RNA template, RNA-cDNA hybrid formed, Degradation of RNA by ribonucleotides, cDNA synthesizedtoi make dbl stranded cDNA |
| Barbara McClintock | discovered Transposons |
| Transposons | jumping genes, direct repeats, this is the action in HIV |
| HIV | retrotransposon, jumping genes |
| RNA poly's | quaternary structure, 2 alpha units, two beta units and a sigma unit. The sigma unit makes it a holoenzyme |
| Upstream Region | Promoters are AT rich, Pribnow Box (TATAAT) at -10. Transcription begins at +1. |
| Termination | hairpin loop-(GC loop) folowwed by AAAA in DNA and UUUU in RNA . Also Rho termination protein |
| Euk RNA Polymerases | (blank) |
| Pol I | in nucleolus |
| Pol II | in nucleoplasm |
| Pol III | in nucleoplasm |
| CATT and TATA(hogness box) | cis acting elements |
| RNA Pol III | found within codong exons |
| Prok Gene Expression | operons-polycistronic mRNA, Constitutive and inducible, coupling transcription/translation |
| Euk Gene Expression | monocistronic, Introns/exons, 3 RNA Poly's, extensive RNA modification, slow changes in gene expression, T/T seperated |
| Amanita phalloides | mushroom producing alpha-amanitin toxin, death cap, blocks RNA poly II, most will die |
| Lariat Processing | a form of hrRNA, conserved sequence at 5' end of exon/intron junction, signals used by U RNA to recognize where to cut ......5' to 2' ester linkage formed |
| 7methyl G cap | 5' to 5' linkage, promotes stability of message, in Euk mRNA |
| Poly A Tail | Euk mRNA at 3' end, additional Adenosine residues 40-200 added. Stabalizes seq., facilitates exit from nucleus |
| Mutations | any change from normal coding sequence of the DNA, a nucleotide change |
| Point mutation | a single base is changed in the DNA producing a single change in the RNA |
| Silent Mutation | these do not affect the AA seq. |
| Missence Mutation | 1 AA is replaced by another AA inthe protein seq. |
| Nonsense mutation | premature termination of a polypeptide chain, change from codon to stop codon |
| Wobble Hyp | to account for degeneracy of a code, H-bonding in 3rd position is flexible, the base Inosine in anticodon can bind with U, C and A |
| AUG | in mRNA codes for methionine |
| Met | all proteins start with this |
| UGG | codes for tryptophan, no other codon for trp |
| UAA, UAG, UGA | nonsense codons, stop translation |
| Euk General | Cap at 5' end binds eIFs and 40s ribosomal subunit+tRNA met mRNA is scanned for AUG. 1st AA= methionine. Initiation factors=eIFs(12+) Ribosomes= 80s |
| Prok General | Shine-Delgarno seq. upstream of AUG binds complementary 16SrRNA. 1st AA=Formyl-Met. Initiation Factor=Ifs(3) Ribosomes=70s |
| Antibiotics | See old tests..matching |
| 3 fates of RER Proteins | Secretion, Lysosome, Membrane Glycoprotein |
| Streptomycin | binds 30S ribosomal subunit of prok. Prevents initiation |
| Tetracycline | binds 30s ribosomal subunit and inhibits binding of aminoacyl tRNA to A site |
| Chloramphenicol | binds to 50s and inhibits peptidyltransferase |
| Erythromycin | binds to 50s and prevents translocation |
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hwhite
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