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Thatcher Biochem
biochemistry unit 2
| Question | Answer |
|---|---|
| replication occurs where in prokaryotes? eukaryotes? | prokaryotes: cytoplasm; eukaryotes: nucleus |
| this polymerase synthesizes the leading strand, is able to proofread, and uses an RNA primer | DNA polymerase delta |
| this polymerase synthesizes the lagging strand, cannot proofread, and uses an RNA primer | DNA polymerase alpha |
| this polymerase fills in the DNA for repair. It does not proofread, or use RNA as a primer | DNA polymerase beta |
| this polymerase is found in the mitochondria and is used to synthesize both leading and lagging strand. It contians a proofreading function but does not use an RNA primer | DNA polymerase gamma |
| metalic cofactor necessary for activation of DNA polymerase | Mg 2+ |
| DNA synthesis always proceeds in which direction? | 5' --> 3' |
| proofreading (exonoculease activity) occurs in which direction | 3' --> 5' |
| which polymerases can perform exonuclease activity? | delta and gamma |
| which model of dna synthesis is followed? | semiconservative, one new daughter plus the parental type |
| describe the difference between the leading and lagging strands | the leading strand is continuously synthesized in the 5'->3' direction by DNA pol delta, while lagging strand is synthesized in 5'-3' in short fragments by DNA pol alpha |
| what are lagging strands called? | okazaki fragments |
| what are "ori" how many of them are present on each chromosome? | origins of replication, many of them exist for every chromosome. |
| prokaryotic vs. eukaryotic ori | prokaryotic: one; eukaryotic: many - this is why it only takes a little longer for hte latter to replicate a genome that is dramatically larger |
| what is a replicon? | a region of eukaryotic genome that is replicated as a unit from one central ori |
| this enzyme binds an ori and serves to open the double helix so the DNA polymerase can begin replication... | helicase |
| this cluster of factors stabilize the single stranded DNA and prevent it from winding back up (supercoiling) | SSBs (single stranded binding proteins) |
| a cluster of factors assembled around helicase that serves to replicate DNA | DNA replication apparatus (this includes DNA polymerases alpha, delta, the "beta clamp", and primase.. it does not include SSBs) |
| this ring like protein wraps around the DNA to stabilize the association of the replication apparatus | beta clamp (this is required for DNA polymerase delta which will "fall off" without it) |
| this enzyme binds the unwound lagging strand template and transcribes short stretches (<15 bp) of RNA primer that provides the necesary 3'OH for DNA polymerase alpha | primase |
| this enzyme removes the RNA primer laid down by primase leaving chunks of missing bps | RNA-ase |
| this polymerase fills in the chunks/gaps of missing bps that were removed by RNA-ase | DNA polymerase beta )these chunks are roughly 20 bp long) |
| this enzyme seals the nicks between the 3' OH and 5' phosphate | DNA ligase (this happens not only after the replacement of DNA for RNA in the lagging strand, but alsoafter DNA excisional repair) |
| this enzyme is responsible for fixing the supercoiling caused by unwinding of DNA (helicase) during replication | topoisomerase |
| this enzyme functions to synthesize the telomere, it contains an RNA reverse transcriptase. It's activity decreases with age, and increased activity of this enzyme is associated with cancer | telomerase |
| this type of RNA encodes polypetide sequences, has the lowest relative abundance, and is synthesized by RNA polymerase II | mRNA (messenger RNA) |
| this type of RNA encodes components of ribosomes, has the highest relative abundance, and is synthesized by RNA polymerase I | rRNA |
| a small RNA molecule that transfers a specific active amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. It has a 3' terminal site for amino acid attachment | tRNA |
| numbering system of transcription | the base at which transcription begins is labeled "1", upstream bases are labeled negative and downstream positive |
| the region of DNA used to activate or repress transcription of a gene, this region is located right next to the gene | promoter region |
| promoter location in regards to which RNA polymerase is being considered | the promoters for Polymerases I and II are adjacent to the gene, while the promoter for polymerase III is within the gene itself |
| the regoin of DNA that regulates transcription of a gene that CAN be moved relative to the gene, it is located a distance away | enhancer |
| the smallest region of a full promoter that wlil drive detectable transcription, they "prime transcription", they drive low level, constitutive transcription | minimal promoter |
| a cluster of proteins konwn as transcription factors that assemble around the promoter to initiate transcription | the initiation complex |
| proteins that form the "core initation complex" | general transcription factors |
| this general transcription factor binds the TATA box (an easily opened adenosine and thymine rich region) | TBP (tata binding protein) |
| promoters and enhancers are actually what? | clusters of recognition sequences, short sequences of DNA that show increased affinity for a specific protein (transcription factor) |
| transcription factors contain 2 domains, what are they? | the DNA binding domain (which has affinity for a specific promoter or enhancer) and a nactivation domain (that has affinity for an RNA polymerase) |
| _____ within a family have similar sequences, but _____ are usually variable | BINDING DOMAINS within a family have similar sequences, but ACTIVATION DOMAINS are usually variable |
| this transcription factor family has 2 a-helices at right angles to eachother, connected by a short linker region. 1 helix has a basic face that binds DNA by wedging into the major groove, contains the homeobox domain | helix turn helix family |
| this transcription factor fmaily has cys and his residues chelated to a central Zn ion, creating "fingers" that wedge into the major groove of DNA | zinc fingers (such as TPB, SP1, and steroid receptors) |
| this transcription factor family have 2 a-helices separated by a longer linker region. they form heterodimers to either activate or repress transcription | helix loop helix |
| which combo of heterodimers will promote transcription? inhibit? | the combination of positive and ubiquitous heterodimer will promote transcription. negative + ubiquitous will inhibit |
| tthis transcription factor family fxn as dimeric proteins that has a leucine every 7 resides. the hydrophobic interactions b/w these leucines form a scissor formation that holds DNA and promotes transcription | leucine zipper |
| where does the cap go? where does the poly a tail go? | 5' cap. 3' poly a tail |
| what does splicing involve? | removal of introns (junk sequences of RNA), rejoining of exons. alternative splicing can lead to more than 1 protein being made from 1 strip of DNA |
| region of the nucleus where ribosomes are produces, not membrane bound, dark spot in nucleus | nucleolus |
| describe the process of rRNA processing (cleaving) | each gene encodes 3 rRNAs. they are all transcribed by pol I as 1 large RNA molecule known as pre-RNA, the introns are then cleaveed away, leaving 3 rRNA exons: 28S, 18S, and 5.8S. A 4th is transcripted separately: 5S RNA (by pol III) |
| these protiens assemble around the rRNA to form large and small subunits of ribosomes | ribonucleoproteins |
| what are some of the unique properties of RNA pol I and pol III promoters? | unlike pol II, the promoters for rRNA and tRNA lack TATA boxes, yet, TBP is still a component of their initiation complex. Pol III promoters are within their genes |
| what is an amazingly simplified summary of the nuclear pore complex function? | DNA is shuttled IN and RNA is shuttled OUT, accomplished using GTP |
| tRNA must have what done to it after it gets out of the nucleus but before it can function in translation? | it must be "charged" or have the specific amino acid bound to it |
| this enzyme charges tRNA | aminoacyl-tRNA synthetase |
| for different codons that specify the same amino acid, it is usually the 3rd base that varies | wobble theory |
| term that describes the fact that codons only specify one amino acid | unambiguous |
| term that describes the fact that most amino acids are specified by more than 1 codon | degenerate |
| the start codon | AUG |
| stop codon | UGA,UAG,UAA |
| recall the mechanism by which new aa residues are added to the polypeptide chain | the tRNA holding onto the polypeptide chain sits in the P site. this chain is then added to the aa bound to the trna that sits in the A site |
| the nascent polypeptide chain comes off the ribosome and binds a receptor on the ER to be shuttled through what to enter the ER? | a protein channel is called a translocon |
| which side of the cytoplasm will a proteins active site face if it is originally facing hte P face? | the protein will face the cytoplasmic side once its vessicle has fused with the cell membrane |
| which side of the cytoplasm will a proteins active site face if it is originally facing the E face | the protein will face the exoplasmic side once its vessicle has fused with the cell membrane |
| effect of a loss of function mutation? | decrease/inactivate gene |
| effect of a gain of function mutation? | increase gene activity |
| mutation that happens in either the 3rd base of a wobbly codon, an intron spliced out, spacer region of chromosome (outside expressed gene), resulting in coding for very similar AA or in a non critical region | silent mutation |
| point mutation resulting in substit. of a pyrimidine for a pyrimidine (or purine/purine) | transition mutation |
| point mutation resulting in pur--> pyrimadine, or vice versa | transversion mutation |
| mutation in which a single base pair is switched which results in the alteration of 1 AA is called? | missense mutation (ex: sickle cell anemia) |
| a mutation in which a bp subst. produces a premature STOP codon that results in a truncated polypeptide is called? | nonsense mutation |
| the insertion/deletion of a sequence thats not a multiple of 3, so that the codon reading frame is altered, resulting in a random aa sequence following the change is called a? | frame shift mutation |
| a ____ is a gross chrom. change that as a result of deletion, insertion, duplication, inversion, and translocation that can be seen under a light microscope | chromosomal aberration |
| which generation is usually affected during a reciprocal translocation | the 2nd generation (happens to gramps, affects his grandkids) |
| this is result from an inversion of the center of chromosome 3, including the centromere | chromosome 3 duplication-deletion syndrome |
| this results from the deletion of the short arm (petite arm) of chromosome 5 | cri-du-chat syndrome |
| to have more sets of parental chromosomes than normal? it is caused by..? | polyploidy is caused by polyspermy |
| to have the wrong number of chromosomes in a parental set? one or more chromosomes has been added or removed? caused by? | aneupoloidy; caused by nondisjunction |
| a failure of chromatids to separate during meitotic anaphase that results in aneuploids? | nondisjunction |
| down syndrome is the result of | trisomy 21 |
| edward syndrome is the result of | trisomy 18 |
| patua syndrom eis the result of | trisomy 13 |
| turner syndrome is the result of | monosomy of the X chromosome (XO) |
| klinefelter syndrome is the result of? | an extra X chromosome (XXY) |
| endogenous mutations occur? | naturally within the cell |
| DNA polymerase infidelity is a result of? | an inherent error/accident of the DNA polymerase. 1 in 10^9 chances |
| system in the liver oxidizes hydrophobic compounds to make them water soluble and therefore excretable. doing this to the wrong molecule may make its products mutagenic (recall the ames test) | cytochrome p-450 system |
| the release of a purine (A or G) by cleavage of the bond at the 1' site of the ribosome | depurination, lack of this correction before the next round of replication will result in its replacement (75% chance of mutation) |
| removal of an AA from a base by oxidation to a keto group... | deamination, with A or C this will result in a transition mutation during the next round of replication... no affect if T or G |
| transient changes in electron configuration of a base, cause it to resemble another base | tautomeric shifts; can lead to transition mutations |
| foreign factors affecting hte cell | exogenous mutagenic agents |
| UV light typically produces what in DNA? | thymine dimers |
| ionizing radiation typically produces what in DNA? | point mutations |
| gamma rays typically produce what in DNA? | chromosomal aberrations |
| alkylating agents such as nitrogen mustart typically result in what in DNa? | this is the addition of methyl or ethyl groups. results in point mutations and chromosomal aberrations |
| strand cleavers such sa peroxides and sulfur compounds typically result in what in DNA? | these sever phosphodiester bonds directly, inducing chrom. aberrations |
| base analogs such as 5-bromouracil typically result in what in DNA? | mimic nucleotides and induce bp substitutions (either transitions or transversions) |
| intercalating agents such as acridine orange or proflavin typically result in what in DNA? | chromosomal aberrations from their "wedging" into the helix |
| insertion elements such as viruses or transposons typically result in what in DNA? | deletions or insertions as well as insertional mutagenesis (disruption of fxn bc of placement inside a gene) |
| if a chromosome is cleaved by mutagenic agents such as gamma rays or peroxides, the strands will automatically be ligated back together by which enzyme? | DNA ligase |
| methylguanin methyltransferase removes methyl groups added to the carbonyl of G by the alkylating agent methylmethane sulfonate...this removal is called what? | direct base repair |
| during excision repair, the enzyme responsible for nicking the site of hte original mutation (thymine dimer) is? | UV specific endonuclease |
| during excision repair, the enzyme responsible for removing a chunk of DNA preceding hte nick made by UV specific endonuclease is? | exonuclease (works in 3'-5' fashion) |
| during excision repair, the enzyme responsible for filling the gape made by exonuclease that removed several nucleotides preceding hte nick made by the UV specific endonuclease is? | DNA polymerase beta (in a 5'-3' fashion) |
| during excision repair, the enzyme responsible for ligatig the backbone after DNA pol. beta filled the gap made by the exonuclease that removed several nucleotides preceding the nick made by the UV specific endonuclease is? | ligase |
| faulty DNA excision repair will lead to which disease? | xeroderma pigmentosum |
| selection summary | stress a group of organisms and the week will die while the strong live. in the case of bacteria, this is creating multiple drug resistent strains of organisms. his is bad. always complete full cycle of antibiotics |
| transport protein mediating facilitated diffusion by single file flow of specific factors thru the protein. they're selective (only allowing one tpe of factor to pass thru), gated and close/open in response to stimuli | channel |
| transport protein passes one factor or sets of factors at a time by undergoing a conformational change that shuttles a factor across the membrane | transporters |
| this type of transport protein mediates active transport by directly hydrolyzing ATP | ATPase pumps |
| this type of transporter transports one factor across the membrane | uniporter |
| this type of transporter simultaneously transports 2 factors across membrane ins the same direction | sympoter |
| this type of transporter simultaneously transports 2 factors across membrane in opp. directions | antiporter |
| this class of ATPase pump uses ATP to pump protons across a membrane, such as in the mitochondria to make ATP | F class pumps |
| this class of ATPase pumps uses ATP to pump ions such as Na/K across a membrane | P class pumps |
| this class of ATPase pump uses ATP to pump protons across a membrane, such as in the case of lysosomes to lower pH | V class pumps |
| this class of ATPase pumps uses ATP to rid a cells of a certain molecule and is seen in the case of MDR bacteria (detoxify) | ABC class pumps |
| recall the mechanism of cystic fibrosis transmembrane conductance regulator | this CFTR *channel*, reqs ATP to open up as well as activation of cAMP domain. once open Cl ions flow out into mucus & the phosph. via cAMP allows Na to go out in the mucus. this elevates osmotic P so H2O goes in mucus. loss of fxn = CF, no watery mucus |
| collection of viscous mucus in the airway provies a nutrient rich environment for what opportunistic bacteria? | pseudomonas aeruginosa |
| recall the mechanism of hte P class ATPase | the E2 domain resides on the inside, E2 is high affinity for factor. Once bound, protein has conf. change n shifts factor to E1 site for discharge and reverts to an open E1 |
| to which side do the E1 and E2 sites face in uniporter? symporter? antiporter? | uniporter - face whatever way necessary to get one molecule to the other side. symporter - e1 and e2 on same side, anti - opposite |
| the function of Na/K antiporter is what | pumps out 3 Na for every 2 K via atp hydrolysis, creating negative charge inside the cell |
| voltage gated Na and K channels function in what process | depolarization causes membrane channels to open, which sends the Na rushing int oth ecells along their gradient |
| thes are used to establish low cytoplasmic ca2+ via the hydrolysis of ATP | Ca2+ ATPases |
| used to control cardiac contraction by controlling Ca2+ by exporting 1 Ca for 3 Na | Na/Ca antiporters |
| coupled transport can be seen in which 2 protein systems that use the hydrolysis of ATP | H/K ATPase and NA/Glucose symporter |
| cellular factor that recognize and bind a specific ligand to induce a response | receptor |
| molecule bound by another molecule such as a receptor | ligand |
| a nutrient ligand secreted by one cell to induc ea response in another cell | intercellular signaling molecule |
| recall thatcher's suggestion that diff fields call the same thing different names | hormone - endocrinologist, growht factor - development, cytokine - immunologist |
| different receptors bound and activated by same ligand, often inducing different cellular responses | isoreceptors |
| for an intercellular signaling molecule to diffuse over a short distance, usually thru interstitial spaces, to induce a response | paracrine signaling |
| for an intercellular signaling molecule to diffuse thru blood over long distances | endocrine signaling |
| these ligands are hydrophobic and can therefore bind/fuse directly with the cell membrane | steroids (cholesterol derivatives prostaglandins retinoic acids (FA derivatives) |
| ligands are hydrophilic and therecore cannot fuse with cell membrane | amino acid derivatives peptides proteins nucleotides |
| whats the only major class of biochemicals NOT used as receptor ligands? | carbohydrates |
| these ligands pass through membranes to bind intracellular receptors | hydroPHOBIC ligands |
| these ligands cannot transverse membranes, must bind extracellular domain of transmembrane receptors | hydroPHILIC ligands |
| the ligands are transported free in the blood plasma | hydroPHILIC ligands |
| these ligands are difficult to store in cells so they tend to be synthesized as needed | hydroPHOBIC ligands |
| require binding proteins to be transported thru the blood | hydroPHOBIC ligands |
| easily stored in gland cell vesicles, serving as preformed stocks to be rapidly secreted as needed | hydroPHILIC ligands |
| rapid response ligands | hydroPHILIC |
| slow response ligands | hydroPHOBIC |
| short half life (seconds to minutes) | hydroPHILIC |
| long half life | hydroPHOBIC |
| recall the factors that can lead to receptor regulation | number, affinity for ligands, affinity for intracellular targets, cellular localization, and amt of membrane fluidity |
| recall mechanism for nuclear receptor activity | steroid fuses and passes thru cellular membrane, binds a nulcear receptor which dimerizes and goes to nucleus to affect gene transcrip. |
| these receptors fxn to transmit an extracellular signal to the intracellular side by straddling the membrane (with a hydrophobic transmembrane domain). they bind a ligand outside that causes a conf. change. inside cell | transmembrane receptors (this conf. change inside cell begins cascade that affects cell fxn) |
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msingal2
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