Term
| What is the difference between the initiation of translation in prokaryotes and eukaryotes? |
|
Definition
| Eukaryotes require capping, splicing, and poly A before transcription is ended and translation begins. Prokaryotes begin translation beforee transcription is ended. |
|
|
Term
| What are the qualities of the CTD on the RNA pol II? |
|
Definition
| "Tail", contains 52 tandem repeats of a 7 AA sequence containing numerous serines which are the sites of phosphorylation. Processing proteins hop from the tail onto the RNA molecule |
|
|
Term
| What is CTP phosphorylated for? |
|
Definition
| Allows dissociation from transcription initiation factors, allows association of RNA processing proteins, to serine active sites |
|
|
Term
| What are processing proteins in DNA transcription? |
|
Definition
| Bound to CTD attracted by phosphorylation, positioned to act on new RNA strand as it emerges. Includes capping factors, splicing proteins, 3' end processing proteins |
|
|
Term
|
Definition
| Responsible for transcription, phosphatases remove phosphates as only dephosphorylated form is the active enzyme. Active enzyme stays on after 3' cleavage, eventually falls off template |
|
|
Term
| When and how does Cap addition occur? |
|
Definition
After ~ 25 nucleotides capped by 7methylguanine, important for transport and translation
1) Phosphatase removes 5' phosphate
2) Guanyl transferase adds GMP 5' to 5'
3) Methyl transferase adds CH3 to the G
Cap is bound by CBC (cap binding complex) |
|
|
Term
| What is the general RXN for RNA splicing? |
|
Definition
1) Branchpoint A attacks 5' splice site and cuts RNA backbone
2) Cut 5' end becomes covalently linked to A, forming lariat
3) Free 3' OH attacks 5' of next exon joining 2 exons, relases lariat
4) Each event removes one intron by 2 phosphoryl transfer RNS, requires no ATP (directly) |
|
|
Term
| What is alternative splicing? |
|
Definition
| Variation of splicing produces different proteins from same genetic material, used by eukaryotes |
|
|
Term
| What are consensus sequences for splicing? |
|
Definition
| Variable, but GU at intron start and AG at infront end are invariant |
|
|
Term
|
Definition
| Small nuclear RNAs, less than 200 nucleotides, U1, U2, U4, U5, U6. Each is complexed with at least 7 proteins. |
|
|
Term
|
Definition
| Complex of snRNA with many proteins, form the spliceosome |
|
|
Term
| How does splicing recognition occur? |
|
Definition
| 5' branch point and 3' sites are recognized through base pairing w/ snRNA's and consensus sequences, breaking & rejoining base pair RXNs require ATP |
|
|
Term
| What happens at the 5' splice site? |
|
Definition
| U1 snRNP binds, triplet of U4/5/6 arrives, lariat is broken, U1 and U4 leave, U5 remains. U6 has replaced U1 snRNP and 3' is cleaved and joined to 5' |
|
|
Term
| What occurs at the branch point during splicing? |
|
Definition
| Branch-point binding protein (BBP) pairs, along w/ U2AF, which is replaced by the U2 snRNP |
|
|
Term
| What does the U5 snRNP accomplish? |
|
Definition
| Undergoes rearrangement after 1st phosphoryl transfer, brings two exons into proximity. Require additional proteins and ATP |
|
|
Term
|
Definition
| Exon junction complex, binds to former intron position, marking successful splice site |
|
|
Term
|
Definition
| Serine / Arginine rich proteins, assemble on exon sequences marking off 3' and 5' sites, recruit U1 and U2AF that delineate upstream and downstream boundaries, this is exon definition. |
|
|
Term
|
Definition
| The delineation of upstream and downstream boundaries by SR proteins |
|
|
Term
|
Definition
| Heterogeneous nuclear ribonucleoprotein complexes package long introns, perhaps mask cryptic splice sites, 30 types, may remove RNA hairpin turns, remain on excised introns marking them for destruction |
|
|
Term
| What is the consensus sequence for 3' end processing? |
|
Definition
| 10-30 nucleotide AAUAA - CA binds CPSF < 30 nucleotide GU region binds CtsF Cleavage occurs, followed by PolyA addition - These proteins travel on RNA Pol II CTD until 3' end processing |
|
|
Term
|
Definition
| Poly-A polymerase adds ~ 200 A nucleotides using ATP as a precursor, does not require a template |
|
|
Term
| What are poly-A binding proteins? |
|
Definition
| Bind to poly-A tail, determine length, some remain bound and aid in protein synthesis |
|
|
Term
| What is the nuclear pore complex? |
|
Definition
| Aqueous channel that connects the nucleus to the cytoplasm, mRNA must be bound by correct proteins to exit nucleus |
|
|
Term
| What is the curved fiber? |
|
Definition
| mRNA forms Balbiani curved fiber to go through neoplasm and exit through pore |
|
|
Term
| What are the correct proteins needed to exit the nuclear pore complex? |
|
Definition
| CBC, EJC, poly-A binding protein, nuclear export receptor |
|
|
Term
| What is nonsense mediated decay? |
|
Definition
| Immediately after nucleus exit, mRNA is checked for a final time to ensure that it is translatable |
|
|
Term
|
Definition
| SImilar to RNA Pol II, synthesizes rRNA, which is about 80% of the cellular RNA. Does not have a C-terminal tail, thus no capping or poly-A |
|
|
Term
| Why are there multiple copies of rRNA genes? |
|
Definition
| There is no translational amplification, thus multiple copies needed. Copies are located in 10 clusters each near the tipe of the pairs of 5 different chromosomes. |
|
|
Term
| What are the types of rRNA? |
|
Definition
4 types, 3 from a single precursor (45S)
-
18S (small SU)
-
5.8S (large SU)
-
28S (large SU)
-
5S from other source
|
|
|
Term
| What modifications does rRNA undergo during formation? |
|
Definition
13,000 nucleotide precursor undergoes approximately 100 methylations, 100 uridine to pseudouridine reactions, which may aid in folding and assembly of final rRNAs. |
|
|
Term
|
Definition
| Small nucleolar RNA's, guide modification of rRNA, contain the modifying enzymes |
|
|
Term
|
Definition
- Site for rRNA processing and assembly into ribosomes
- Not membrane bound, aggregate of macromolecules
- rRNA genes in 10 clusters each near tirp of 5 chromosome pairs, tips segregate during mitosis and coalesce as nucleolus reforms
- other RNAs produced here, including tRNAs |
|
|
Term
| What is the pyruvate dehydrogenase complex? |
|
Definition
| Composed of 3 enzymes, 8.5 x 10^6 Daltons, the size of a ribosome. The complex requires 5 coenzymes, is highly regulated, and generates energy. |
|
|
Term
| What are the 3 enzymes in the pyruvate dehydrogenase complex and what are their qualities? |
|
Definition
- Pyruvate dehydrogenase: 12 dimers: requires TTP coenzymes, performs oxidative decarboxylation of pyruvate
- Dihydrolipoyl transacetylase: 8 trimers: requires lipoamide, transfer of acetyl group to CoA
- Dihydrolipoyl dehydrogenase: 6 dimers: requires FAD, performs regeneration of oxidized form of lipoamide and transfer of e- to NAD+
|
|
|
Term
| What is the coenzyme for Pyruvate dehydrogenase? |
|
Definition
| TTP (thymidine pyrophosphate) |
|
|
Term
| What is the coenzyme for dihydrolipoyl transacetylase? |
|
Definition
|
|
Term
| How does pyruvate enter the mitochondria? |
|
Definition
| Via the monocarboxylate transporter in the inner mitochondrial membrane |
|
|
Term
| How is the pyruvate DH complex inhibited? |
|
Definition
| Products provide feedback inhibition, e.g. acetyl CoA, NADH |
|
|
Term
| How the pyruvate DH enzyme inhibited / activated? |
|
Definition
By a kinase and phosphate pairing mechanism. When phosphorylated enzyme is inactive, when not phosphorylated enzyme is active.
Products stimulate kinase (NADH, acetyl CoA)
Substrates inhibit kinase (CoASH, NAD, pyruvate)
ADP is also an inhibitor of kinase!
Phosphotase is activated by Mg2+, Ca2+, insulin effects |
|
|
Term
| What are the steps in the pathway for fatty acid -> acetyl CoA? |
|
Definition
- adenylation
- acelation of CoASH
- transfer to carnitine
- transport through inner membrane
- reconjugation with CoA
- beta-dehydrogenation
- hydration
- thiolytic cleavage yielding acetyl-CoA and acyl-CoA w/ 2 less carbons
|
|
|
Term
|
Definition
| Transporter assures integrity of cytosolic and mitosolic CoA pools, used for fatty acids 10-20 carbons long |
|
|
Term
| What 2 enzymes are most important in the transfer of fatty acids into the mitochondria? |
|
Definition
| CPT I and II, carnitine palmitoyl transferases |
|
|
Term
| What is the general process of beta-oxidation of a fatty acid? |
|
Definition
- Oxidation, 1.5 ATP generated from FADH2 formation
- Hydration
- Oxidation, 2.5 ATP generated from NADH formation
- Thiolytic cleavage, 10 ATP generated from acetyl-CoA
|
|
|
Term
|
Definition
- center of metabolism
- 10 ATP for each cycle
- does NOT require O2
- 8 enzyme steps, few defects
- amphibolic pathway, oxidation and synthetic functions
- terminal "furnace" for oxidation of acetyl-CoA
|
|
|
Term
| What is the sequence of reactions in the TCA cycle? |
|
Definition
- acetyl CoA + oxaloacetate -> citrate
- citrate -> isocitrate
- isocitrate -> alpha-ketoglutarate (isocitrate dehydrogenase)
- alpha-ketoglutarate -> succinyl CoA (alpha-ketoglutarate dehydrogenase)
- Succinyl CoA -> succinate (succinyl CoA synthetase)
- succinate -> fumarate (succinate dehydrogenase)
- fumarate -> malate
- malate -> oxaloacetate
|
|
|
Term
| What is the key regulating enzyme in the TCA cycle? |
|
Definition
| Isocitrate dehydrogenase, catalyzes reaction of isocitrate to alpha-ketoglutarate, releases CO2, reduces NAD+ to NADH |
|
|
Term
| What is succinyl CoA synthetase? |
|
Definition
| Catalyzes succinate synthesis from succinyl CoA, releases HS-CoA, requires H2O, Pi, and converts GDP to GTP. Free energy of -8 makes this energetically favorable. |
|
|
Term
| What is succinate dehydrogenase? |
|
Definition
| Catalyzes reaction of succinate to fumarate, formation of a double bond. Oxidizes FAD to FADH2. This is Complex II in the electron transport chain! |
|
|
Term
| How is isocitrate DH regulated? |
|
Definition
| Allosteric regulation by ATP and ADP (- and +) |
|
|
Term
| What is the number of codons? |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| transfer RNA, ~80 nucleotides long, adaptors that recognize and bind to both codon and AA |
|
|
Term
|
Definition
| by RNA Polymerase III, trimmed from larger precursor. Approx. 50 different types of modifications help folding |
|
|
Term
|
Definition
| Set of 3 nucleotides on tRNA that pairs with complementary mRNA codon |
|
|
Term
| What is the 3' end of tRNA? |
|
Definition
| Region where matched AA is attached |
|
|
Term
| What is Wobble base pairing? |
|
Definition
-
Some tRNA can pair with more than one codon
-
Some codons have more than one tRNA
-
Some AA's only require accurate base pairing at first 2 positions, last position is "wobble"
|
|
|
Term
| How are codons "named" and read? |
|
Definition
| Codons named 5' to 3' on tRNA ("backwards"), codons on mRNA read 5' to 3' as well |
|
|
Term
| What are amino-tRNA synthetases? |
|
Definition
| Adapters that link correct AA's to 3' end of tRNA, usually there is one synthetase per AA |
|
|
Term
| How does tRNA recognition occur? |
|
Definition
| AAtRNA synthetase uses nucleotide binding pockets - most recognize anticodon sequence though some recognize 3' end. |
|
|
Term
| How do AAtRNA synthetase specificity occur? |
|
Definition
-
Correct AA has high affinity for nucleotide binding pocket
-
Incorrect larger AA is excluded from pocket
-
Editing forces incorrect tRNA to 2nd pocket that excludes correct AA and hydrolyzes all others
|
|
|
Term
| How does polypeptide chain growth occur? |
|
Definition
- Peptide bond formed between OH group on end of chain and amino group on incoming AA
- Through attachment to tRNA each AA carries the activation energy needed for addition of next AA
- protein synthesized from N term -> C term
|
|
|
Term
| What are the general characteristics of ribosomes? |
|
Definition
- 2 subunits, 50 proteins & 4 RNA molecules
- subunits are assembled on nucleolus
- subunits are separate when not synthesizing
- 1 mistake every 10,000 AA's
- attached to ER or free in cytoplasm
|
|
|
Term
| What are the rates of prok. versus euk. translation? |
|
Definition
| 20 AA/sec for prok, 2 AA/sec for euk. |
|
|
Term
| What does the small ribosomal subunit do? |
|
Definition
|
|
Term
| What does the large ribosomal subunit do? |
|
Definition
|
|
Term
| What is the order of events in translation as peptide elongation occurs? |
|
Definition
- tRNA carrying next AA bind to A site via base pairing (P & A sites occupied)
- Peptide bond formation between AA's at P and A sites catalyzed by ribosomal peptidyl transferase
- Large subunit moves relative to mRNA and the two P & A tRNA's are shifted to the E and P sites
- Another serires of conformational changes moves the small subunit three nucleotides and resets ribosome
|
|
|
Term
| What is ribosomal peptidyl transferase? |
|
Definition
| Responsible for catalyzing peptide bond between AA's at P and A sites |
|
|
Term
| What are elongation factors? |
|
Definition
|
|
Term
| What are the order of events in the action of EF-Tu? |
|
Definition
- GTP bound EF-Tu/aa-tRNA binds to A site where codon/anticodon pairing tested, conformation of GTP-EF-Tu allows pairing but prevents peptide bond formation
- Pairing is tested by an rRNA in the small SU that forms h-bond with correct pair
- correct pair triggers GTP hydrolysis & EF-Tu leaves ribosome, charged tRNA then binds to A site
|
|
|
Term
| Following GTP hydrolysis in translation, how does the time period between tRNA addition vary? |
|
Definition
| There is a time delay which is shorter for a correct versus incorrect pair, this allos time for incorrect pair to dissociate |
|
|
Term
| What is the action of EF-G? |
|
Definition
| Binds to ribosome and hydrolyzes GTP while switching ribosome back into position to accept new tRNA |
|
|
Term
| What are the names for EF-Tu and EF-G in eukaryotes? |
|
Definition
|
|
Term
| What is the level of bond consumption for each peptide bond formed in translation? |
|
Definition
| 2 high energy bonds to charge tRNA, 2 to read code on ribosome, 0 for chemistry of peptide bond |
|
|
Term
| How is the ribosome considered a ribozyme? |
|
Definition
-
2/3 RNA and 1/3 protein
-
RNA is central while proteins are on the surface
-
A, P, E sites formed by rRNA
-
catalytic peptidyl transferase formed by pocket in 23S rRNA reminiscent of protein catalyst
|
|
|
Term
How is eukaryotic protein synthesis initiated? |
|
Definition
- AUG codon specifies methionine @ N-term, removed later by protease
- Meth-tRNA is loaded onto small SU w/ eukaryotic initiation factors (eIFs)
- Small SU binds to 5' end of mRNA molecule recognized by the 5' cap and eIF4E and eIFG
- Small SU moves 5' to 3' along mRNA looking for AUG to set reading frame (90% from first AUG in sequence)
- eIFs dissociate from small SU to allow large SU to come in
- Initiator tRNA is now bound to P site leaving the A site vacant for protein synthesis to begin
|
|
|
Term
| How is the efficiency of AUG recognition determined? |
|
Definition
| Dependent on the surrounding sequence, if recognition site differs from consensus significantly ribosome may proceed to second or third AUG. |
|
|
Term
|
Definition
| Allows formation of different proteins from same gene, by means of starting from a different AUG start codon |
|
|
Term
| What is the difference between bacterial initiator tRNA and eukaryotic initiator tRNA? |
|
Definition
| Bacterial utilize formyl methionine, not methionine. |
|
|
Term
| What is the Shine Delgarno sequence? |
|
Definition
| Used by bacteria, mRNA ribosome binding site just upstream from AUG, binds 16S RNA of small SU - 5'-AGGAGGU-3' |
|
|
Term
| Where and why does translation occur during transcription? |
|
Definition
| In bacter there is no nucleus to exit, and ribosomes attach to mRNA as soon as 5' exits polymerase |
|
|
Term
|
Definition
| UAA, UAG, UGA - these do NOT specify an AA |
|
|
Term
| What are release factors in termination? |
|
Definition
| Bind to any ribosome w/ stop codon in A site, structures of release factors are similar to tRNAs |
|
|
Term
|
Definition
| In eukaryotes, large assemblies of ribosomes on one mRNA, as close as 80 nucleotides apart |
|
|
Term
| What is translational recoding? |
|
Definition
| Selenocysteine (AA 21) can be incorporated using tRNA that recognizes a stop codon |
|
|
Term
|
Definition
| Reading frame change produces different protein. Example: HIV RT & integrase from same mRNA as capsid proteins |
|
|
Term
| How are ribosomes affected by antibiotics? |
|
Definition
| Bacterial ribosome has binding sites for antibiotics, interfere with protein synthesis |
|
|
Term
| How does nonsense mediated decay function? |
|
Definition
| Occurs near the nuclear envelope and performs a test-round of translation. Ribosome aided by surveillance proteins, good proteins released to cytoplasm, bad proteins are degraded. |
|
|
Term
| What would be an example of a bad mRNA that would be degraded by nonsense mediated decay? |
|
Definition
| If start codon was next to a stop codon, and the EJC fell after the stop codon. |
|
|
Term
| What fraction of human disease can be attributed to nonsense codons? |
|
Definition
| 1/3 human disease. In heterozygotes truncated transcripts must b e removed to prevent accumulation of possibly TOXIC protein in order to allow non-affected protein to function |
|
|
Term
| What is a molten globule? |
|
Definition
| Starting point for tertiary folding, molten globule beings immediately after domain emerges from ribosome to form alpha helices and beta sheets. |
|
|
Term
| What type of incorrect folding can provide signals for chaperone proteins? |
|
Definition
| Hydrophobic residues on the proteins surface can provide signals |
|
|
Term
| What are chaperone classes in eukaryotes? |
|
Definition
|
|
Term
|
Definition
- EARLY ACTING
- aided by hsp40, ATP-hsp70 binds to string of ~ 7 hydrophobic residues before protein leaves the ribosome
- upon hydrolysis of ATP hsp70 clamps tightly
- after dissociation of hsp40 hsp70 dissociates induced by rebinding of ATP
- repeated cycles of hsp70 bind and release, helping protein to refold
|
|
|
Term
|
Definition
- ACTS AFTER COMPLETED SYNTHESIS
- misfolded protein captured by hydrophobic interactions along rim of barrel
- binding of ATP/protein cap increase diameter of barrel, partially unfold protein and captures it for refolding
- after ~ 15s, ATP hydrolysis weakens complex
- 2nd ATP binding causes ejection - REFOLDED OR NOT!
|
|
|
Term
| What are other names for hsp60? |
|
Definition
| TCP-1 in cytosol of vertebrates, GroEL in bacteria |
|
|
Term
|
Definition
| Formed by hydrophobic interactions, if refolding fails protein destroyed by proteosome |
|
|
Term
|
Definition
- ATP dependent protease, 1% of cellular protein
- hollow cylinder (20S core), stack of 4 rings
- 19S cap is 6 subunit rings, through which target proteins are red by ATP hydrolysis
- core contains proteases, which cleave protein into short peptides
- Example includes AAA unfoldase
|
|
|
Term
|
Definition
| 76 AA's, protein for degradation must be ubiquitated to be degraded by proteosome |
|
|
Term
| How does ubiquitylation occur? |
|
Definition
- E1 ubiquitin activation enzyme prepares UB. for binding to other proteins by forming THIOESTER bond between C-term of UB & cysteine on E1
- E1 transfer UB to a cysteine of E2 of the E2-E3 ligase complex
- UB transferred to target protein via LYSINE residue
- Succeeding UBS. transferred to target by E1 through a LYSINE residue on previous UB to form UB chain recognized by proteosome
|
|
|
Term
| How do the E2-E3 complexes differ? |
|
Definition
| Hundreds of these complexes can recognize different signals including denaturation, misfolding, abnormal AA's, and even some normal proteins marked for degradation. |
|
|
Term
| What is special about the CFTR protein? |
|
Definition
| A 3' nucleotide deletion, a loss of F, causes protein to not fold or be glycosylated properly, making it a target for proteosomes. |
|
|
Term
| How does aggregation in Huntington's occur? |
|
Definition
| CAG repeat up to 100 times, causes polyglutamine. |
|
|
Term
| How does aggregation occur in Alzheimer's? |
|
Definition
| Stacks of beta sheets that are resistant to proteolysis |
|
|
Term
| What is the electron transport chain? |
|
Definition
| Series of redox catalysts within the IMM that transport electrons from respiratory substrates to oxygen while capturing the free energy of the oxidation/reduction reactions to effect ATP synthesis. |
|
|
Term
|
Definition
| Protons are extracted concurrent with electron removal and pumped from the matrix across the inner membrane to form an electrochemical gradient, providing energy for ATP synthesis |
|
|
Term
| What is ΔE° for the transfer of an electron between 2 redox pairs? |
|
Definition
| ΔE (acceptor) - ΔE (donor) |
|
|
Term
| What are the electron carriers used in the ETC? |
|
Definition
- flavoproteins
- cytochromes
- copper (complex IV)
- ubiquinone (coenzyme Q)
|
|
|
Term
|
Definition
| Used as an e- carrier in the ETC, contain tightly bound FMN or FAD, transports 1-2 e- |
|
|
Term
|
Definition
| Heme containing proteins in the ETC, transport 1 e- from Fe2+ |
|
|
Term
| How is copper used in the ETC? |
|
Definition
| In Complex IV, used to transport 1 e- |
|
|
Term
|
Definition
| Coenzyme Q, in the ETC is used to transport 1-2 e- |
|
|
Term
| What is Complex I in the ETC? |
|
Definition
| NADH-CoenzymeQ Reductase. Transfers 2 e- and 2 H+ to CoQ, enough energy to pump 4+ from matrix to IMM allowing for synthesis of 1 ATP. Converts NADH to NAD. |
|
|
Term
| Is there free energy gain as e- transfer between Complexes I and II occurs? |
|
Definition
| No, free energy liberated in this e- transfer is insufficient to pump H+ across the IMM, thus there is no gain in free energy. |
|
|
Term
| What is Complex II in the ETC? |
|
Definition
| Succinate DH, converts succinate to fumarate, and FADH2 to FAD. |
|
|
Term
| What is Complex III in the ETC? |
|
Definition
| CoQH2-Cytochrome C Reductase - pumps 4 H+ into IMM |
|
|
Term
| What is Complex IV in the ETC? |
|
Definition
| Cytochrome C Oxidase - converts 1/2O2 to H2O, pushes 2 HT+ into IMM |
|
|
Term
| What is Complex V in the ETC? |
|
Definition
| ATP synthase, catalyzes reaction of ADP + Pi -> ATP and brings H+ into the cell |
|
|
Term
| What is oxidative phosphorylation? |
|
Definition
| The coupling of ATP synthesis with electron transport in the respiratory chain |
|
|
Term
| What is the net RXN in mitochondria? |
|
Definition
NADH + H+ (1/2)O2 --> NAD+ + H2O
ADP + Pi --> ATP + H2O |
|
|
Term
| What is respiratory control in relationship to the connection between the ETC and ox.phos? |
|
Definition
| ATP demand regulates its synthesis, which regulates the rate of electron transport. More ATP equals greater O2 consumption, NO ATP equals NO O2 consumption |
|
|
Term
| What is the proton/charge gradient? |
|
Definition
| Obtained by the transfer of 2e- from NADH -> (1/2)O2 and pumping of 10 H+ across membrane, establishes gradient, generates H+ motive force |
|
|
Term
| What does the pH gradient across the IMM allow for? |
|
Definition
| Drives phosphate and pyruvate import |
|
|
Term
| What does the voltage gradient in the IMM allow for? |
|
Definition
| Drive ADP -> ATP exchange |
|
|
Term
|
Definition
A 2 domain protein composed of F1 and F0 subunits. F1 is the peripheral enzyme complex containing the ATP & ADP binding sites, as well as catalytic centers (ATPase activity), present in matrix bound to the IMM.
The F0 protein is embedded in IMM and provides H+ channel. |
|
|
Term
|
Definition
| ATP synthase inhibitor, inhibits O2 consumption |
|
|
Term
| What are the effects of 2,4 dinitrophenol? |
|
Definition
| Dissipates H+ gradient, e- transport continues without ATP synthesis, heat is generated. |
|
|
Term
What are the differences among cell types in an organism caused by? |
|
Definition
| Not the loss or gain of genetic information, bur rather accumulation of different levels of RNA and protein molecules. |
|
|
Term
| How is transcription analyzed by DNA microarrays? |
|
Definition
| mRNA collected from cells is converted to cDNA which is then labeled with a fluorescent probe. Red spots indicate that the gene is expressed in sample 1 at a higher level than in sample 2. Green spots indicate that the gene is expressed in sample 2 at a higher level than in sample 1. Yellow spots indicate the gene is expressed equally in both samples. Dark spots indicate no expression in either sample |
|
|
Term
| How does cluster analysis work? |
|
Definition
| Coordinately regulated genes in human fibroblasts are serum-deprived than reintroduced to serum. Compared to controls, red is increased expression and green is decreased expression. |
|
|
Term
| What does polyacrylamide gel electrophoresis allow for? |
|
Definition
| Protein diversity analysis. Red dots common to both samples, blue dots specific to one. |
|
|
Term
| How do regulatory proteins in transcription function? |
|
Definition
-
Recognize short stretches of DNA, about 20 nucleotides of defined sequence.
-
Read the sequence as a pattern of molecular features on the surface of the DNA molecule
-
Make weak contacts with DNA at the individual level but 20 or more contacts make the interaction specific and strong
-
Generally present in small amounts
-
MOST BIND TO MAJOR GROOVE
|
|
|
Term
| Where are the edges of each base pair in the DNA helix? |
|
Definition
| Exposed at the surface of the DNA helix and the major and minor grooves reveal distinct patterns of hydrogen donors and acceptors as well as hydrophobic patches |
|
|
Term
| What is the simplest and most common DNA binding motif found in both humans and prokaryotes? |
|
Definition
The helix-turn-helix.
C-terminal recognition alpha helix fits into the major groove where it contacts the edges of the bases. The N-terminal helix is a structural component that positions the recognition helix. |
|
|
Term
| How do the helix-turn-helix proteins bind DNA? |
|
Definition
| As dimers, the recognition helices bind to two similar half sites separated by one turn of the helix |
|
|
Term
| What are homeodomain DNA binding proteins? |
|
Definition
Contain helix-turn-helix domains and play fundamental role in development. Three alpha-helices packed together by hydrophobic interaction:
Helices 2 & 3 comprise the H-T-H
Helix 3 binds in the major groove
Helix 1 binds in the minor groove |
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|
Term
| What is the structure of a zinc finger? |
|
Definition
| An alpha helix and beta sheet held together by a zinc molecule, often works in clusters. Typically has cys-cys-his-his that grasps the zince. |
|
|
Term
| How do zinc finger proteins function? |
|
Definition
| The alpha helix of each finger contacts the major groove, the protein is arranged as three direct repeats. |
|
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Term
|
Definition
| This tumor supressor gene uses protruding peptide loops to read nucleotide sequences, rather than alpha helices and beta sheets. Recognizes nucleotides in both major and minor grooves. |
|
|
Term
| What is the leucine zipper? |
|
Definition
| Two alpha helices, one from each monomer, dimerize by hydrophobic interactions forming a coiled coil, usually between leucines, to form an inverted Y-shaped structure. Each monomer binds to a specific DNA sequence in the major groove. |
|
|
Term
| What are heterodimer proteins used for? |
|
Definition
| Heterodimers can recognize a hybrid sequence, as opposed to homodimers which recognize symmetric sequences. |
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|
Term
| Heterodimerization is an example of ... |
|
Definition
| Combinatorial control where a combination of proteins controls a cellular process. |
|
|
Term
| What are helix-loop-helix motifs? |
|
Definition
| Can form homodimers and heterodimers. The two monomers are held together in a four helix bundle, each monomer contributes two alpha helices connected by a flexible loop. One helix of each monomer contacts the DNA. |
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|
Term
| What is a very common protein-DNA interaction? |
|
Definition
| Due to geometry of hydrogen bond acceptors, guanine can be unambiguously recognized by the side chain of ARG in the major groove. Can also be recognized by Ser, His, and Lys |
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|
Term
| What is a gel mobility shift assay? |
|
Definition
| Used to identify protein that bind to specific DNA sequences. An extract from an antibody-producing cell line was mixed with a radioactive DNA fragment of 160 nucleotides of regulatory sequence from the antibody light chain gene. |
|
|
Term
| How does DNA affinity chromatography work? |
|
Definition
| Can be used to purify proteins that bind to specific DNA sequences, protein can then be analyzed by mass spectrometry, and the AA sequence and thus the gene determined |
|
|
Term
| What is DNA footprinting? |
|
Definition
| A DNA-binding protein is allowed to bind to DNA, random cleavage by nuclease or chemical is followed by removal of the protein and separation of DNA strands. The footprint is where no cleavage is observed. |
|
|
Term
| How can DNA sequence for a protein with unknown DNA binding specificity be determined? |
|
Definition
| By using a random pool of short DNA double helix fragments. |
|
|
Term
| What is chromatin immunoprecipitation? |
|
Definition
| Used to identify DNA sites bound to regulatory proteins in living cells. Can also be used to identify positions of histones in living cells. Regulatory protein bound to DNA is cross-linked to DNA with formaldehyde, cells are lysed, DNA is broken down into small fragments, DNA with specific protein of interest is precipitated with antibodies, amplified by PCR. |
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|
Term
| How does E. coli determine which of its 4300 proteins to express? |
|
Definition
| Regulated by the available nutrients in the environment |
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|
Term
| How is the bacterial tryptophan operon regulated? |
|
Definition
| By the presence of its end product tryptophan. When the operator is recognized and bound by a repressor protein, access to the RNA polymerase is blocked. In the presence of two tryptophan molecues the repressor will bind. |
|
|
Term
| How does the tryptophan repressor protein function? |
|
Definition
| A helix-turn-helix regulatory protein, changes in the conformation caused by the binding of two tryptophan allow it to fit on the operator and thus block transcription. |
|
|
Term
| When are transcriptional activators used? |
|
Definition
| When RNA polymerase binds poorly to bacterial promoters, or the polymerase has difficulty opening the helix. |
|
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Term
|
Definition
| The catabolite activator protein, CAP, a helix-turn-helix, activates genes that enable E. coli to use alternative carbon sources when glucose is limiting. |
|
|
Term
| How is the CAP protein activated? |
|
Definition
| When glucose levels fall in the cAMP levels increase and cAMP binds to CAP enabling CAP to bind to its specific sequence next to target promoters and activate transcription. When cAMP levels fall as glucose levels increase, CAP dissociates and transcription is no longer activated. |
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|
Term
| How is the lac operon regulated. |
|
Definition
| Positively and negatively - positively by CAP which is bound in the absence of glucose. In the absence of lactose, the lac repressor protein is bound to the operator and transcription of the lactose transport proteins is shut down. In the presence of lactose, the concentration of allolactose increases which in turn binds to the repressor releasing it from the DNA. |
|
|
Term
| How does cooperativity function in the lac operon? |
|
Definition
| Because there are several lac repressor binding sites, cooperative binding of the repressor is required for complete repression. |
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|
Term
| How does the lac repressor bind two operators? |
|
Definition
| The lac gene has three operators, one primary and two secondary. DNA looping stabilizes protein-DNA interactions and allows a single tetrameric lac repressor to bind two operators simultaneously |
|
|
Term
| What can DNA looping accomplish? |
|
Definition
- Allows repressor/activator protein to bind to more than one operator
- Allows two different proteins bound to different sections of DNA to contact each other, e.g. bound activator can loop over and contact bound polymerase
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|
|
Term
|
Definition
| Interchangeable subunits of RNA polymerase that control transcription activation. Different sets of sigma factors recognize different sets of promoters thus enabling a large set of genes to be turned off and another large set to be turned on just by switching sigma factors. |
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|
Term
| How can DNA inversion switch gene expression? |
|
Definition
| A specific recombination event inverts DNA and changes the orientation of the promoter and a switch from one type of protein to another (e.g. one type of flagellin). This is used to avoid immune surveillance. |
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|
Term
| What is the difference in transcription factors in eukaryotes versus prokaryotes? |
|
Definition
| While bateria RNA polymerase only requires sigma factor, eukaryotes require five general TF's (27 subunits) |
|
|
Term
| Because eukaryotes do not have operons, each gene ... |
|
Definition
| must be separately regulated. |
|
|
Term
| What are the same for all RNA polymerase II genes? |
|
Definition
| The mediator protein and transcription factors. However, the other regulatory proteins are different among the genes. |
|
|
Term
| What is the typical design of eukaryotic gene activator proteins? |
|
Definition
| A structural motif that recognizes and binds to DNA, and activation domain that accelerates the rate of transcription initiation. |
|
|
Term
| How do gene activatory proteins in eukaryotes promot the assembly of the transcription complex? |
|
Definition
| By attracting, positioning, and modifying the general transcription factors, mediator, and RNA pol II at the promoter, as well as CHANGING THE CHROMATIN STRUCTURE AROUND THE PROMOTER! |
|
|
Term
| How can gene activator proteins act synergystically? |
|
Definition
| If factor A speeds up transcription 100-fold and factor B speeds it up 100-fold, if they are both bound they enhance transcription up to 10,000 fold. |
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|
Term
| How does eukaryotic transcription repression often function? |
|
Definition
| Repressors do not usually compete with RNA polymerase II. Repressors can bind competitively with activators (stealing their binding spot), can bind to the activator itself (masking activation surface), or can interaction with transcription factors directly with DNA looping. Repressors can also act by returning nucleosomes to their pretranscriptional form. |
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|
Term
| What happens when repressors return nucleosomes to their pretranscriptional form? |
|
Definition
| Chromatin remodeling complexes are recruited, the affinity of nucleosomes for TFIID is reduced, thus proteins which keep chromatin in a transcriptionally inactive state are recruited. |
|
|
Term
| What are coactivators/corepressors? |
|
Definition
| Proteins that do not bind directly to DNA but to bound complexes. These proteins can interact with chromatin remodeling complexes, histone modifying enzymes, RNA pol, or general transcription factors. |
|
|
Term
| How can weak interactions between multiprotein activator/repressor complexes be overcome? |
|
Definition
| Binding is nucleated by the DNA itself. |
|
|
Term
| What is regulation by committee? |
|
Definition
In some cases an elaborate protein-DNA structure formed, and the gene is expressed only when the correct combination of proteins is present.
Requires an ARCHITECTURAL protein to bend DNA allowing other proteins to bind so that the structure can enable transcription. |
|
|
Term
| What is competition with respect to transcription? |
|
Definition
| Competition occurs between activation and repression |
|
|
Term
| How are transcriptional regulatory mechanisms typically controlled? |
|
Definition
| Extracellular signals communicated across the plasma membrane |
|
|
Term
| What does the pattern of gene expression within a cell result from? |
|
Definition
| Complicated molecular computation that the intracellular control netork performs in response to the cell's surroundings |
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|
Term
| How is the beta-globin gene regulated? |
|
Definition
| Activities of regulatory proteins are though to change during development, only a particular combination triggers transcription of the gene. GATA-1 is found only in a few cell types including RBC's. GATA-1 binding sites overlap with those of other regulatory proteins, excluding their binding. Once bound regulatory proteins recruit the proteins involved in transcription and the genes are transcribed at extremely high rates. |
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|
Term
| How does expression of beta-like globin genes change during development? |
|
Definition
| Epsilon in early embryo, gamma in later embryo and fetus, sigma and beta in the adult. Each gene has its own set of regulatory proteins to turn the gene on at the appropriate time in the appropriate tissue. The product of each of the genes combines with an alpha globin chain to form hemoglobin in RBC's, each with different O2 binding properties. |
|
|
Term
|
Definition
| Locus control region, a shared control region, which helps to achieve their high rate of transcription. |
|
|
Term
| How does an LCR function? |
|
Definition
| Proteins bound to the LCR help attract chromatin remodeling complex, histone-modifying enzymes and components of the transcription complex that act by DNA looping with proteins bound to the specific regulatory regions of each globin gene. Also contains a barrier sequence that prevents the SPREAD OF HETEROCHROMATIN. LCR's can also be present upstream from other highly transcribed regions. |
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|
Term
| What does the barrier sequence in an LCR do? |
|
Definition
| Prevents the spread of heterochromatin. |
|
|
Term
| How is the LCR affected in certain types of thalassemia? |
|
Definition
| The beta-globin locus has deletions that remove all or part of the LCR. Although the gene and other regulatory regions are intact, the gene remains transcriptionally inactive even in erythroid cells. |
|
|
Term
|
Definition
| DNA sequences that bind specific proteins and prevent regulatory proteins from influencing distant genes. |
|
|
Term
| What are barrier sequences? |
|
Definition
| DNA sequences that prevent the spread of heterochromatin |
|
|
Term
| How do insulators function? |
|
Definition
| May serve as decoys tying up transcriptional machinery, or may anchor DNA to the nuclear envelope interfering with DNA looping between an enhancer and the wrong promoter. |
|
|
Term
| What appears to be responsible for the wide variety of life on earth? |
|
Definition
| Changes in gene regulation rather than the acquisition of new genes. |
|
|
Term
| How is the expression of large groups of genes coordinated? |
|
Definition
In bacteria accomplished by operons functioning under a single promoter.
In eukaryotes, each gene has its own promoter. Even though most eukaryotic regulatory proteins act as a committee, a SINGLE regulatory protein can be decisive in switching any particular gene on and off simply by completing the combination needed. |
|
|
Term
| How is gene expression controlled by the glucocorticoid receptor? |
|
Definition
• To bind regulatory sites in DNA, the glucocorticoid receptor must first form a complex with a glucocorticoid steroid hormone such as cortisol; in the absence of cortisol, the receptor is retained in the cytoplasm and is unavailable to bind to DNA
• Cortisol is released during times of starvation and intense physical activity and it stimulates liver cells to increase the production of glucose from amino acids
• To do this the liver must increase the expression of many different genes which for maximal expression requires the binding of the hormone-glucocorticoid receptor complex |
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|
Term
| What is DNA methylation and what does it accomplish? |
|
Definition
| Methylation of cytosine in adjacent CG sequences allows the pattern of DNA methylation to be passed on to daughter cells. Methyltransferases act on CpG only when opposing CpG is methylated. Regulates gene expression by repressing, methylation of promoter or regulatory sequence can interfere with TF binding. |
|
|
Term
| What does imprinting usually do to genes? |
|
Definition
| Silences genes, exceptions includes insulin-like growth factor gene, Igf2, where the reverse is true. |
|
|
Term
| How is the regulation of the Igf2 gene accomplished? |
|
Definition
| Only paternal imprinted copy of Igf2 is transcribed. In the maternal copy, CTCF binds to insulator element, preventing transcription. However, Methylation of the insulator on the paternal chromosome block CTCF binding and allows a distant enhancer element to activate transcription of the Igf2 gene. |
|
|
Term
| What are methylated C's prone to? |
|
Definition
| Deamination which results in conversion to a T. |
|
|
Term
| What site is responsible for x chromosome inactivation? |
|
Definition
| A single site in the middle of x chromosome called the X-Inactivation-Center (XIC) |
|
|
Term
|
Definition
| XIC, in the middle of the x chromosome, about 10^6 base pairs, seeds the formation of heterochromatin and facilitates its bidirectional spread. Initiates and spreads x-inactivation. |
|
|
Term
| What does the XIC gene encode for? |
|
Definition
| An unusual RNA molecule, XIST RNA (x-inactivation specific transcript), expressed solely from the inactivated x and necessary for its inactivation. |
|
|
Term
| What is the purpose of XIST? |
|
Definition
| XIST RNA remains in the nucleus and coats the inacctive X chromosome, the spread of XIST RNA correlates with spread of gene silencing suggesting that XIST RNA drives formation and spread of heterochromatin. About 10% of the genes on the X chromosome remain active. |
|
|
Term
| What are the characteristics of inactive X heterochromatin? |
|
Definition
- XIST RNA utilization
- contains a specific variant of histone 2A, which is ubiquitylated
- it is hypoacetylated on histones 3 & 4
- is methylated at a specific position on histone H3
- has its DNA methylated
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|
|
Term
| What is transcriptional attenuation? |
|
Definition
A regulatory mechanism that causes premature ending of transcription. Can often be an attenuating region of DNA that occurs before the operator, when product is present a terminator stem loop structure forms in the mRNA and RNA polyemerase falls off the template.
Under limiting Trp and Trp-tRNA, adjacent Trp codons stall the ribosome and the downstream mRNA assumes a different stem loop structure that allows transcription to continue. |
|
|
Term
| What is transcriptional attenuation in the case of HIV? |
|
Definition
| RNA polymerase poorly processive due to poor phosphorylation, makes short transcripts. These short transcripts become translated to TAT protein, which bind to mRNA Tar region and phosphorylate CTD of RNA pol, resulting in increased processivity and formation of full length transcripts. |
|
|
Term
|
Definition
| Short sequences of RNA that change their conformation when they bind to a small molecule and the resulting conformational change is used to regulate transcription. Often located at the 5' end of the mRNA and fold during mRNA synthesis. |
|
|
Term
| What percentage of human genes produce multiple proteins by means of alternative splicing? |
|
Definition
|
|
Term
| What, other than vertebrates, often uses alternative splicing as a means of obtaining different proteins? |
|
Definition
|
|
Term
| How can 3' end processing regulate protein production? |
|
Definition
| A change in the site of RNA transcript cleavage and poly-A addition can change the C-terminus of a protein. This type of switch determines whether an antibody produced by a B lymphocyte will be secreted or remain membrane bound. |
|
|
Term
| How do b lymphocytes produce, from the same gene, antibody proteins which will either be secreted or remain membrane bound? |
|
Definition
| Depending on whether the RNA is cleaved as a short or long transcript, different stop codons will be utilized, resulting in different ends on the antibodies (hydrophobic or hydrophilic). |
|
|
Term
|
Definition
| Alters the sequence of mRNA after transcription. Common in mitochondra of trypanosome and plants and affects over 100 genes in humans. Deaminates adenine to produce inosine or deaminates cytosine to produce uracil. |
|
|
Term
| How does RNA editing occur in mammalian cells? |
|
Definition
| Deamination of A to inosine in RNA by ADAR (Adenosine Deaminase Acting on RNAs) can change splicing patterns or the meaning of codons (inosine pairs with C instead of T). |
|
|
Term
| What is an example of RNA editing? |
|
Definition
| in the pre-mRNA encoding a transmitter-gated ion channel in the brain, a single RNA edit changes Glu to Arg. Since the affected amino acid lies on the inner wall of the channel, the change alters the calcium permeability of the channel. |
|
|
Term
| How is the ADAR enzyme attracted? |
|
Definition
| A double stranded complementary sequence attracts the enzyme |
|
|
Term
| What are ADR1 and ADR2 required for? |
|
Definition
| Liver for RBC development and brain development, respectively |
|
|
Term
| In viruses, what is an example of the action of ADAR? |
|
Definition
| mRNA synthesized from the genomic minus strand of hepatitis delta satellite virus encodes small delta antigen required for replication. ADAR acts on the full length plus strand copy which leads to an edited mRNA and synthesis of the large delta antigen which is required for virus maturation. |
|
|
Term
| How does HIV overcome the problem of moving unspliced mRNAs into the cytoplasm? |
|
Definition
| These would normally be degraded, however, one of the spliced mRNA code for REV that binds the Rev Response Element in the unspliced viral RNA, but Rev interacts with the nuclear pore export protein exportin 1, and directs unspliced viral RNA through the nuclear pores. |
|
|
Term
| Where are attenuation and riboswitches found? |
|
Definition
|
|
Term
| In prokaryotes, how can translation be easily repressed? |
|
Definition
| By the binding of a specific translational repressor to the Shine-Delgarno sequence. |
|
|
Term
| How is selection of the initiating AUG codon in eukaryotes determined? |
|
Definition
| Because there are no Shine-Delgarno sequences in eukaryotes, selection of AUG is determined by proximity to the 5' cap where the small ribosomeal subunit binds and begins scanning for the initiating AUG. |
|
|
Term
| How can a eukaryote utilize translational repressors? |
|
Definition
| A repressor can bind to the 5' end inhibiting translational initiation, others can bind to the 3' and decrease initiation by interfering with communication between 5' cap and 3' poly-A tail. Eukaryotes also use micro RNAs that bind to specific mRNAs and reduce protein production. |
|
|
Term
| How can viruses make different proteins from the same RNA post-translationally? |
|
Definition
| The (+) strand genome serves itself as the message. The message is translated into a polyprotein that is cleaved into functional proteins by a viral encoded protease. |
|
|
Term
| How is global regulation of protein synthesis achieved? |
|
Definition
| By the phosphorylation of the translation initiation factor, eIF2. |
|
|
Term
| What does eIF-2 require to be released? |
|
Definition
| eIF2 is bound tightly to GDP, and requires guanine nucleotide exchange factor eIF-2B to release GDP so that GTP can bind and eIF2 can be recycled |
|
|
Term
| What happens if eIF2 is phosphorylated? |
|
Definition
| It cannot be reused, thus protein synthesis is slowed down, important in mammalian cells to respond to stressful conditions and allow cells to enter non-dividing resting stage |
|
|
Term
|
Definition
| When the efficiency of translational initiation at the first AUG is poor the scanning ribosomal subunits will skip to the second or third AUG ... this can produce the same protein without a signal sequence at the N-terminus. |
|
|
Term
| What are IRES and what do they do? |
|
Definition
| Interal Ribosome Entry Sites are present in internal sequences in the mRNA molecules, these are several 100 nucleotides in length that fold into special structures and bypass the requirement for the 5' cap. |
|
|
Term
| What translation factor recognizes the 5' cap? |
|
Definition
|
|
Term
|
Definition
| By encoding a protease that cleaves the eIF-4G factor into a truncated form that can no longer interact with the cap but is competent at IRES. |
|
|
Term
| When do eukaryotic cells use IRES? |
|
Definition
| During mitosis and apoptosis where overall translation is greatly diminished. |
|
|
Term
| What is the stability of mRNA? |
|
Definition
| Bacterial very unstable, generally only average half-life of 3 minutes. Eukaryotes mRNAs are much more stable, up to 10 hour half life. Shorter half life eukaryotic proteins often code for regulatory proteins whose production rates need to be flexible. |
|
|
Term
| What are the two major degradation pathways in eukaryotes? |
|
Definition
Gradual shortening of the ~200 polyA tail by deadenylation (DAN) occurs then the pathway diverges-
- At 25 polyA, cap is removed and RNA is degraded from 5' end
- RNA continues to be degraded from 3' end
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|
|
Term
| What is another mechanism used by eukaryotes for mRNA degradation? |
|
Definition
| the mRNA contains a specific nucleotide sequence in the 3'UTR, usually AU rich, that is cleaved by a specific endonuclease |
|
|
Term
| How do iron-mediated translational controls function? |
|
Definition
Mediated by translational repression and mRNA stability.
When iron is high, a cell increases synthesis of ferritin to bind more iron and decreases synthesis of transferrin to import LESS iron. Acontinase binds to a stem loop in the respective mRNAs. |
|
|
Term
|
Definition
| Can repress protein synthesis and accelerate deadenylation of mRNA, work post-transcriptionally |
|
|
Term
|
Definition
miRNA precursors are transcribed by RNA pol II and are capped and polyA'd. The DROSHA complex cleaves an mRNA stem loop structure into a pre-miRNA of 82 nucleotides. This is exported and processed into ~22 nt duplexes by the DICER COMPLEX.
These duplexes are assembled into RISC (Rna Inducing Silencing Complex) complexes and are converted into single strands. The miRNA guides the RISC complex to the mRNA to be regulated. |
|
|
Term
| How does RISC decide what mRNA will be degraded? |
|
Definition
| If base pairing with miRNA base pairing with mRNA is extensive, >7 bps, the mRNA is sliced and degraded. If not, the mRNA is transferred to P-bodies where is it sequestered and eventually degraded. Following release of the RISC complex from the mRNA it can seek out another mRNA and thus catalytically destroy many mRNAs. |
|
|
Term
|
Definition
| A component of the RISC protein |
|
|
Term
| What sequence does a miRNA target? |
|
Definition
|
|
Term
|
Definition
| RNA-Induced Transcriptional Silencing complex, which binds complementary nascent transcripts and attracts proteins that modify histone and direct formation of heterochromatin. This process maintains the heterochromatin around centromeres and limits the accumulation of transposable elements by keeping them in the heterochromatin. |
|
|
Term
| What can siNRA be bound by? |
|
Definition
|
|
Term
|
Definition
An uncoupling protein which is found in brown adipose tissue, it is activated in response to intracellular signalling events evoked by a "cold" stimulus.
Localized exclusively in the IMM, dissipate the H+ gradient across the IMM by acting as a proton conducting protein, transporting H+ back into the matrix.
Uncoupling of ATP synthesis from electron transport allows the free energy to be released as heat. |
|
|
Term
| What can poison Complex I in the ETC? |
|
Definition
|
|
Term
| What can poison Complex III in the ETC? |
|
Definition
|
|
Term
| What are poisons of Complex IV in the ETC? |
|
Definition
|
|
Term
| Problems with CoQ (ubiquinone) lead to ... |
|
Definition
| Uncoupling of Complex I & II, and II & III. Leads to seizures, progressive muscle weakness, and accumulation of lactate in cerebrospinal fluid. |
|
|
Term
|
Definition
| Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes. Category of conditions caused by defects in oxidative phosphorylation. |
|
|
Term
| What organ is affect most by problems with electron transport? |
|
Definition
|
|
Term
| What does copper deficiency lead to, especially in neonates? |
|
Definition
| A failure to synthesize adequate amount of cytochrome c oxidase |
|
|
Term
| What is the coenzyme of alpha-ketoglutarate dehydrogenase? |
|
Definition
|
|
Term
| Oxidatative decarboxylation of pyruvate renders ...? |
|
Definition
|
|
Term
| What are the metabolic fates of pyruvate? |
|
Definition
| Alanine, oxaloacetate, acetyl coA, lactate |
|
|
Term
| What does carboxylation of pyruvate render? |
|
Definition
|
|
Term
|
Definition
| Lactate is always produced by the reduction of pyruvate catalyzed by lactate dehydrogenase. Lactate is always REMOVED by the reversal of this process. |
|
|
Term
| What are the causes of heterogeneous metabolic disease? |
|
Definition
| Pyruvate DH complex defects in subunits, as well as pyruvate DH, or PDHC deficiency |
|
|
Term
| Why are neurological issues so prevalent in PDHC diseases? |
|
Definition
| Because the brain depends on carbohydrate utilization for energy more than any other organ. |
|
|
Term
| How is a deficit in the PDH complex compensated for? |
|
Definition
| Increased glycolysis leading to excess lactate |
|
|
Term
| Why does it make sense that necrotic lesions would develop in areas where there is poor vascularization? |
|
Definition
| Poor vascularization leads to poor removal of lactate |
|
|
Term
| Why might chronic situations arising from excess lactate lead to neuronal cell death? |
|
Definition
| Localized lactic acidosis, intracellular ATP depletion |
|
|
Term
| Restriction of dietary carbohydrate has been effective in alleviating symptoms of lactic acidosis in patients with a genetic defect in E1 of PDHC. Why? |
|
Definition
| Carbohydrate will be "spared" for use by the brain. |
|
|
Term
| What does dicholoroacetate do to PDHC? |
|
Definition
| Inhibits PDHC kinase leading to dephosphorylation and activation of any functional E1. |
|
|
Term
|
Definition
| Organic compounds produced by MICROBES that inhibit the growth of other microbes, usually secondary metabolites |
|
|
Term
| Antibiotics can confer ...... on the species that produces them. |
|
Definition
| Selective growth advantage. Still, antibiotics have never been discovered in soil at high enough concentration to be inhibitory to neighboring cells and are usually only detected when microbes are grown in the lab. |
|
|
Term
| What is an explanation for the existance of antibiotics among microbes? |
|
Definition
| Evolutionary vestiges, leftovers of obsolete pathways. |
|
|
Term
|
Definition
| The first synthetic antibiotics (1930's), similar to folic acid, a nucleic acid precursor. Active against bacteria because they make their own folic acid. |
|
|
Term
|
Definition
| Discovered by Alexander Fleming, from a fungus, inhibited strep. Beta-lactam drug. |
|
|
Term
| What type of antibiotics make up half of the antibiotics worldwide? |
|
Definition
| Beta-lactam drugs including penicillins, cephalosporins, carbapenems, etc. |
|
|
Term
| What is selective toxicity? |
|
Definition
| Antibiotic must be more toxic to the pathogen than to the host |
|
|
Term
| What is therapeutic ratio? |
|
Definition
| Highest dose that controls infection and patient can tolerate without toxic side effects, ideally has high therapeutic ratio |
|
|
Term
|
Definition
| Minimum inhibitory concentration, smallest amount of antibiotic needed to inhibit growth, usually performed with tube dilution technique |
|
|
Term
| What is the Kirby-Bauer test? |
|
Definition
| Test various concentrations of the antibiotic, antibiotic diffusese off disc into lawn on plate, creating zone of inhibition. However, antibiotic may not diffuse in the chosen growth medium. |
|
|
Term
|
Definition
| Combination of the MIC test and diffusion susceptibility test |
|
|
Term
| What do broad-spectrum antibiotics usually target? |
|
Definition
| Highly conserved cellular processes, including translation, metabolism, etc. |
|
|
Term
| What happens to large numbers of bacteria exposed to antibiotics over time? |
|
Definition
| Most die off, but resistance emerges |
|
|
Term
| How many tons of antibiotics are used worldwide every year? |
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Definition
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|
Term
| What two factors are antibiotic resistance correlated with? |
|
Definition
| Inappropriate extensive usage, and inadequate dosage or time of administration |
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Term
| What is natural resistance? |
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Definition
| Microbe lacks the structure that an antibiotic inhibits, e.g. chlamydia and mycoplasmas lack peptidoglycan cell walls, OR microbe is impermeable to antibiotic |
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Term
| What is acquired resistance? |
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Definition
| New resistance genes on plasmids and transposons, can be transferred through conjugation or transformation, also new mutations on chromosomal genes |
|
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Term
| What are 5 mechanisms of antibiotic resistance? |
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Definition
| Reduced permeability, inactivation of antibiotic, alteration of target, development of resistant biochemical pathway, efflux |
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Term
| What are examples of enzymatic inactivation of antibiotics? |
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Definition
| beta-lactamases (bla genes), chorolamphenicol acetyltransferases (cat genes), streptomycin 3'adenylyltransferase - aminoglycoside-modifying enzymes |
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Term
| How can beta-lactamases be overcome? |
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Definition
| By inhibitors including beta-clavulanate, or derivatives that protect ring from cleave |
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Term
| MRSA is an example of what type of resistance? |
|
Definition
| Modification of targes - cell wall synthesis is catalyzed by multiple penicillin-binding proteins (PBPs) some that have acquired penicillin resistance. |
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Term
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Definition
| Encodes PBP2a that doesn't bind to beta-lactam drugs, encoded on SCCmec mobile genetic elements (staphylococcal cassette chromosome mec) |
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|
Term
| What are MDR efflux pumps? |
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Definition
| Can be specific for one antibiotic or multiple, MDR can arise from increased amounts of the pump, or mutation causing increased efficiency |
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|
Term
| How many genes does E. coli have? |
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Definition
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|
Term
| How is the packaging problem overcome in prokaryotic chromosomes? |
|
Definition
|
|
Term
| What type of antibiotics inhibit supercoiling? |
|
Definition
| Quinolones (ciprofloxin, etc.) |
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|
Term
| Where do plasmids in eukaryotes typically arise from? |
|
Definition
| Partial or completely viral |
|
|
Term
| What can plasmids encode for? |
|
Definition
| Cell invasion, hemolysin, enterotoxin, antibiotic resistance |
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|
Term
| What is the cornerstone of recombinant DNA technology? |
|
Definition
| The use of plasmids for propagation of "foreign" DNA |
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|
Term
|
Definition
| Movement of DNA from one chromosome site to another, low occurence, requires transposon - can also jump to plasmids and be transferred to other cells |
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Term
| What are the three types of transposable elements in prokaryotes? |
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Definition
| insertion sequences (IS) can only transpose, transposons (Tn) contain additional DNA besides the IS element can contain antibiotic resistance genes that can move from cell to cell, and Mu - double-stranded DNA bacteriophage that inserts into host genes |
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|
Term
| What do insertion sequences require in prokaryotes? |
|
Definition
| Transposase enzyme (Tnp), recognizes, cuts, and ligates DNA, interacts with short terminal repeats |
|
|
Term
| What is replicative versus nonreplicative transposition? |
|
Definition
| Copy paste versus cut paste mechanisms. |
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|
Term
|
Definition
| Eterotoxins in E. coli, can be encoded by bacteriophage |
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|
Term
|
Definition
| Ability to uptake naked DNA, natural phenomenon |
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|
Term
| What is competency with respect to transformation? |
|
Definition
| The ability of cell to uptake DNA, several proteins required for uptake, not all cells can be transformed. Can be naturally competent or induced. |
|
|
Term
| What is the general mechanism of transformation? |
|
Definition
| Binding of ds DNA to cell surface, one strand degraded, RecA mediates homologous recombination into chromosome |
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|
Term
| What is the difference between generalized and specialized transduction? |
|
Definition
| In gen. piece of chromosomal DNA can be incorporated into phage and transduced into other cell, in specialized transduction only chromosomal DNA adjacent to integration site of phage can be incorporated into phage. |
|
|
Term
| What is the protein found in the F pilus? |
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Definition
|
|
Term
| A filamentous DNA phage binds to .. |
|
Definition
| Pilus tip, have ss circulator DNA genome |
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|
Term
| An icosahedral RNA phage binds to ... |
|
Definition
| Pilus sides, have ss linear RNA genome |
|
|
Term
| What are the genes regulating conjugation and where are they found? |
|
Definition
| Only on conjugative plasmids, the tra genes, in E. coli known as the F plasmid |
|
|
Term
|
Definition
| Regulates DNA strand transfer, generates single strand cut on plasmid, becomes covalently bonded to 5' end and navigates strand to recipient cell |
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|
Term
|
Definition
| High frequency of recombination, has F plasmid integrated into the chromosome. Hfr strains transfer (mobilize) chromosomal DNA to other cells |
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|
Term
| Is horizontal DNA transfer in bacteria uni or bidirectional? |
|
Definition
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