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Micro section 2
| Question | Answer |
|---|---|
| genome | all genetic material that defines an organism |
| bacterial genome size | between 0.5-10 Mb |
| plasmids | circular fragments of DNA in bacteria |
| Griffith | in vitro transformation using dead bacterial genetic material, horizonal gene transfer |
| Avery, Macleod, McCarthy | followed up Griffith by demonstrating that DNA stored hereditary information |
| DNA components | phosphates, nitrogenous bases, sugars |
| Watson and Crick | double helical structure of DNA, wobble hypothesis |
| DNA structure | polymer of nucleotides, connected to each other by phosphodiester bonds |
| Hydrogen bonding | allows complementary base interactions that allow the two phosphodiester backbones to come together in an antiparallel fashion, forming double helix |
| Nucleoid | bacteria pack their DNA here in a series of loops or domains |
| Supercoiling | so that DNA is compact |
| Gyrases/topoisomerases | enzymes that increase or decrease supercoiling of DNA |
| Semiconservative | Replicated DNA contains one parental strand and one new synthesized strand |
| Initiation | starts at the origin of replication |
| OriC | the origin of replication |
| elongation | two replication forks move in opposite directions around the chromosome |
| termination | at defined sites located opposite to the origin |
| ter | termination sites |
| direction of new DNA synthesis | 5 to 3 |
| DNA polymerase | main replication enzyme, adds nucleotides to make DNA daughter using info from mother strand. ONLY WORKS 5 to 3 |
| leading strand | after replication, the 3 to 5 strand that's replicated in the 5 to 3 direction |
| lagging strand | after replication, the 5 to 3 strand that's replicated discontinuously in stages, produces Okazaki fragments |
| Helicase | separates the two DNA strands, unzips the H-bonds |
| Primase | lays down a short stretch of complementary RNA/RNA primers |
| Rnase H | removes RNA primers |
| Ligase | repairs the nicks in backbone |
| restriction enzymes/endonucleases | enzymes produced by various strains of bacteria that cleave/restrict foreign phage DNA at palindromic sequences, make "sticky ends" |
| Phages/bacteriophages | viruses that attack bacteria |
| sticky ends | DNA ends that can be spliced together and join foreign strands of DNA |
| agarose gel electrophoresis | used to analyze the DNA fragments obtained by treatment with restriction enzymes |
| DNA sequencing | the most commonly used DNA sequencing method, relies on Sanger dideoxy strategy |
| Sanger sequencing | ddNTPs terminate DNA synthesis so you can determine DNA sequence, based on enzymatic synthesis of DNA in vitro |
| ddNTP | dideoxyribonucloside, prevents strand extension at 3 end |
| Sanger | uncovered amino acid sequence of insulin, RNA phage replication, DNA sequencing method |
| Central dogma | Genetic information flows from DNA to RNA to protein, producing a phenotype |
| messenger RNA/ mRNA | RNA made during transcription, like 5% of RNA, half life is less than 3 mins, it rapidly recycles |
| Ribosomal RNA/ rRNA | used during translation, most of the RNA, half life is hours |
| Transfer RNA/ tRNA | used during translation, 15% total RNA, half life is hours |
| transcription | reading DNA template to make RNA copy |
| translation | decoding RNA to assemble proteins |
| RNA polymerase | key enzyme of transcription, carries out transcription by making RNA copies of a DNA template strand |
| Core polymerase | RNA polymerase component, adds nucleotides |
| Sigma factor | RNA polymerase component, recognizes the promoter sequence, only needed in initiation, finds beginning of gene |
| holoenzyme | core RNA polymerase and sigma factor |
| consensus sequences | recognized by sigma factors at -35 and -10, promotor regions |
| initiation | RNA pol holoenzyme binds to promotor by help of sigma factor, closed RNA pol complex becomes open as a transcription bubble |
| elongation | RNA chain extended by addition of ribonucleotides using info in template strand, temporarily base pair to template strand |
| termination | RNA pol detaches from DNA after transcript is made |
| Rho dependent | relies on rho protein to terminate |
| rho independent | requires GC rich region of RNA and no extra factors |
| genetic code | series of 64 triplet codons that instruct ribosome to add specific amino acids to growing polypeptides or to STOP translation |
| translation | requires mRNA to carry codons, ribosomes, and tRNA |
| ribosome subunits | rRNA and proteins |
| small subunit | 30s |
| large subunit | 50s |
| binding sites for tRNA | E site, P site, A site |
| E site | exit, binds a tRNA recently stripped of its polypeptide, for uncharged tRNA |
| P site | site of ribosomal peptidyltransferase activity, binds only met-tRNA |
| A site | acceptor, binds incoming aminoacyl-tRNA, for charged tRNAs, STOP codon causes release protein activation |
| 16s | sub-unit highly useful in phylogenetic studies, part of 30s |
| Svedberg coefficient | relies on particles mass, density, and shape. bigger particles sediment faster in ultracentrifuge so have higher S values |
| Aminoacyl tRNA syntheses | join amino acid(uncharged) to tRNA at 3 accepter with proper anticodon, results in loaded/charged tRNA ready to join ribosome at A site |
| met-tRNA | the initially loaded tRnA that delivers methionine at P site |
| anticodon | hydrogen bonds with the mRNA codon specifying an amino acid |
| hairpin loops | anticodon loop, t loop, d loop |
| wobble hypothesis | says that flexible base-pairing at the third position of an mRNA codon allows one tRNA to recognize multiple codons. |
| peptidyl transferase | ribozyme and catalytic rRNA within P site |
| C terminus | end of a protein/polypeptide with a free carboxyl (–COOH) group. During translation, new amino acids are added, so proteins are built N → C. |
| polysomes | Multiple ribosomes translating the same mRNA molecule at the same time, allowing the cell to make many copies of a protein quickly. |
| rifamycin B | Transcription, Binds bacterial RNA polymerase → inhibits transcription initiation. |
| Actinomycin D | Transcription, Binds DNA → inhibits transcription elongation. |
| streptomycin | Translation, Inhibits 70S ribosome formation → inhibits translation. |
| Tetracycline | Translation, Prevents aminoacyl-tRNA from binding to the A site → inhibits translation. |
| Chloramphenicol | Translation, Inhibits peptidyl transferase → prevents peptide bond formation. |
| transformation | importing free DNA into bacterial cells, recipient cells need to be competent, food, repair, adaptation/evolution. |
| conjugation | transfer of DNA from one bacterium to another, cell to cell contact, require plasmids |
| plasmids | contain genes necessary for plus formation and DNA export, can also contain antibiotic resistance genes |
| transduction | bacteriophages carry host DNA from one cell to another |
| generalized transduction | can transfer any gene from donor to recipient |
| specialized transduction | can transfer only a few closely linked genes between cells |
| types of gene transfer | transformation, conjugation, transduction |
| lytic cycle | virus copies and kills cell |
| lysogenic cycle | virus copies, doesn't kill, can be lytic later |
| lysogenic toxins | salmonella, cholera, botulinum, diphtheria, e.coli, staphylococcus aureus |
| restriction | CUT → restriction enzymes/endonucleases cut foreign DNA |
| modification | PROTECT → methylation protects the bacteria’s own DNA from being cut |
| point | single nitrogenous base is changed |
| transition | one purine or pyrimidine is converted to another |
| silent | doesn't lead to change in amino acid |
| missense | changes one amino acid to another |
| nonsense | changes an amino acid codon to a STOP codon |
| frameshift | shifts the reading frame of a gene |
| deletion/insertio | bases are deleted or added, if not in multiple of 3 can cause frameshift |
| operon | series of genes organized to be controlled by the same promoter, control gene expression at transcription level |
| operator | Dna region near the promoter where the repressor binds |
| repressor | binds regulatory DNA and prevents transcription, gene OFF |
| promoter | region that binds RNA polymerase and starts transcription |
| allosteric | molecular shape shifting/ function change |
| palindromic sequence | same DNA sequence forward and backward when read 5-3 |
| start codon | AUG |
| exonuclease | cleaves linear DNA, removes mismatched bases, excises at ends |
| topoisomerase | alters DNA conformation between open circles and supercoiled |
| Cas9 | cleaves invading phage DNA, guided to matching sequence by guide RNA before cut |
| peptidyltransferase | bonds amino acids into polypeptides/proteins, is a ribozyme |
| high melting temp | more GC |
| Doudna and charpentier | defined CRISPR systems in prokaryotes |
| Nathans and smith | discovery of restriction endonuclease |
| male bacterium | f+ |
| what happens when DNA enters bacterial cell | non self replicating plasmid/linear DNA degrade or integrate into chromosome by recombination |
| innate bacterial immunity | restriction modification system using endonuclease |
| adaptive bacterial immunity | CRISPR- cas system, remembers phage DNA and targets it in the future |
| CRISPR spacers | pieces of DNA from past infections stored between repeat sequences |
| purines | AG |
| pyrimidines | CTU |
| DNA rep errors | DNA made 5-3 but checked 3-5, exonuclease removes mismatched bases |
| mutation causes | mutagens, chemical agents, irradiation |
| BER | repairs individual damaged bases. glycosylase removes damaged base, endonuclease cuts backbone, DNA polymerase replaces, ligase seals |
| NER | removes patch of nucleotides around damage. UvrABC endonuclease cuts patch, polymerase fills gap, ligase deals |
| T-t dimers | DNA damage caused by UV light, bonds adjacent thymine bases together, repaired by NER |
| gene expression | process of using genes to make RNA or proteins |
| Bacteria/gene expression | they control it bc they want to save energy by not making proteins they don't need |
| levels of gene expression control | DNA, transcription, post-transcription, translation, and post-translation |
| DNA level control | microbes can mutate/flip FNA to turn genes on/off. most drastic and least reversible |
| phase variation | DNA sequence is flipped, changes surface antigen so bacterium can avoid immune response |
| transcriptional control | uses regulatory proteins to control whether genes are transcribed |
| activator | binds regulatory DNA and stimulates transcription, gene ON |
| anti-sigma factor | inhibits sigma factor, decreases transcription |
| post-transcriptional control | controls mRNA stability to determine how much protein gets made |
| RNases | degrade mRNA, prevent it from being translated to protein |
| Monod and Jacob | operon |
| translational control | fine tunes gene expression during translation, can respond to amino acid levels in the cell |
| attenuation | regulation that senses amino acid levels and increases/decreases transcription of genes needed to make it |
| tryptophan attenuation | low tryptophan=ribosome stalls=transcription continues=more tryptophan producing enzymes made |
| post-translational control | controls proteins after they've already been made by modifying/destroying them |
| chemical modification of proteins | phosphorylation, methylation, or acetylation can activate/deactivate proteins |
| protein cleavage | cuts or destroys a protein after translation |
| lac operon | operon involved in biodegradation, substrate present, ON |
| trp operon | operon involved in biosynthesis, product present, OFF |
| structural genes | genes in an operon that code for proteins used for specific function |
| regulator gene | gene that codes for the repressor protein |
| b-galactosidase | enzyme that breaks lactose into glucose and galactose |
| no lactose | repressor binds operator and transcription OFF |
| lactose present | lactose binds repressor, repressor leaves operator, transcription ON |
| lacZ | b-galactosidase, breaks down lactose |
| lacY | permeate, brings lactose into cell |
| lacA | transacetylase, helps detoxify lactose metabolism byproducts |
| no tryptophan | repressor inactive, can't bind operator, transcription ON, cell makes tryptophan |
| tryptophan present | binds repressor, activates repressor, repressor binds operator, transcription OFF |
| autoinducer | chemical signal secreted by bacteria that accumulates as bacterial pop increases |
| low cell density | low autoinducer concentration and bacteria act individually |
| high cell density | autoindicers accumulate and reach threshold, alter gene expression and act as group |
| pseudomonas aeruginosa/quorum sensing | at high cell density, quorum sensing activates biofilm formation and virulence factors that damage tissue |
Created by:
odetteschnell7