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genetics 1
| Question | Answer |
|---|---|
| silent mutation | when phenotype not changed |
| misense mut | may cause a change |
| nonsense | early stop, truncated protein-shortened protein |
| frame shift | addition or deletion |
| AA | 64 possible, 1 start, 3 stop, 60 other 19 AA |
| allele | any of several forms of a gene, hereditary |
| metagenomics | ? |
| transcriptome | a collection of all the messenger RNA in a particular cell |
| proteome | the entire complement of proteins found in an organism over its entire life cycle |
| Nucleic acids | nucleotide polymers |
| nucleotides | composed of N base, Pentose monsaccharide, Phosphate |
| Chargaff’s rules | ratios of A T and G C always 1 , Adenine of one chain forms 2 h bonds with thymine of the other chain, and guanine forms 3 H bonds w cytosine |
| Comparison of genomes | Differ in nucleic acid composition and stranding. Viruses: ssRNA, dsRNA, ssDNA, dsDNA Cells: dsDNA Differ in structure. Circular or linear Differ in gene arrangement. Monocistronic or polycistronic Exons and Introns Differ in ploidy state. Dif r |
| viral genome | only one to have RNA as sole genetic material, only autonomously replicating organisms to have single-stranded DNA, ds DNA and RNA, ss DNA and RNA |
| Pro genome | Chromosomes are usually single, circular, haploid dsDNA,Chromosome located in nucleoid region , Primary metabolic functions, Introns generally absent |
| Eu genome | linear ds DNA wound around histones, |
| chromosome | series of nucleosomes form chromatin and when condensed, |
| Cell replication | synthesis of DNA (genomic, mt, cp, plasmid, prophage) from DNA is a semi-conservative process. |
| Viruses and viroids: | synthesis of DNA or RNA by semi-conservative or conservative processes depending on genomic material. |
| Starting point of replication | Bacteria: origin of replication (ori) and ends at a terminus Archaea have single and multiple origins. Eukaryotes have multiple starting sites = autonomously replicating sequences |
| Rep bidirectional | Replication fork theta structure or rolling circle. linear chromosomes require end lengthening |
| Rate | Bacteria 750-1,000 base pairs/second. Eukaryote 50-100 base pairs per second. Bacteria 1 starting point Yeast 400 starting points in 15 chromosomes. |
| Rolling circle replication | common to transfer of DNA in bacterial conjugation, and replication of plasmids, viroids and some viruses. Concatameric nucleic acid is made by rolling circle replication. After four rounds, how long is the concatamer? 5 |
| Replication | The process of replication is similar in cells; however, the replication enzymes and proteins differ. Eukarya and Archaea have similar proteins, than to Bacteria. |
| replisome | several proteins involved, E. coli has about 30 |
| type III | primary DNA polymerase used as replicase |
| polymerase | reads 3 to 5 |
| nucleotides | are added 5 to 3 |
| proofread fidelity for bacteria | 1 in a billion |
| helicase | local, unwinds |
| single stranded binding proteins | keep strands apart |
| topoisomerases | upstream, relieves tension |
| primase | syn an RNA primer |
| protein binding | start, A T rich b/c its easier to seperate 2 H bondsq |
| E. coli replication | DNA A proteins bind to 4 DNA A boxes within origin of replication, DNA A uses ATP to seperate the strands of DNA |
| E. coli replication 2 | DnaC, called the helicase loader, delivers DnaB, which is composed of six identical subunits, to the template. One DnaB hexamer clamps around each single strand of DNA at oriC, forming the prepriming complex. |
| E. coli replication 3 | DnaB is a helicase, and the two molecules then proceed to unwind the DNA in opposite directions away from the origin. |
| Common replication origins | 1. Replication origins are unique DNA segments that contain multiple short repeated sequences. |
| Common rep origins 2 | 2. Proteins control the initiation of DNa replication by directing the rep of machinery to sites on DNA. They assembly DNA plms |
| Common rep origins 3 | Origin regions usually contain an AT-rich stretch. |
| Topoisomerase | moves ahead of the replication fork and transiently break one (TP I) or both (TP II) strands to relieve the tension. |
| DNA gyrase | unwinds DNA during replication, and introduces negative supercoils for compaction. |
| Single-strand DNA-binding (SSB) proteins | stabilize ss conformation, prevent hairpin helices |
| primosome | formed by primase, syn short strand of RNA that acts as a primer for DNA plms III, creates 2 rep forks |
| DNA plms | 2 core polymerases for DNA synthesis and 3΄→5΄ proofreading. fidelity 2 tau subunits that link the polymerases. β clamps that tether the polymerases to the DNA strands. proccessivity γ complex acts to connect β clamps to DNA |
| Leading strand | 3 to 5, Continuous process and requires a single primer at start. |
| Lagging strand | 5 to 3, Discontinuous process requiring several RNA primers, SSB proteins, clamps and a loop of DNA. |
| Okazaki fragments | 1000-2000 bac, 100 in Eu |
| DNA plms job | add dNTP to 3' hydroxl group to primer strand hydrogen-bonded to the template |
| replisome | to work DNA on lagging strand must be looped back upon itself to create a 3΄→5΄ direction, each fragment requires a primer and new clamp |
| Lagging strand completion | DNA Polymerase I removes the RNA primer from 5΄→3΄ direction and inserts dNTPs until it reaches the next stretch of DNA. DNA ligase joins the free 5΄phosphate of the Okazaki fragment to the 3΄-OH of the new DNA. |
| catenanes | hooking of chromosomes, resolved by topoiso Iso |
| Linear chromosome problem | no primer on 3' so the 5΄ complementary terminus is shortened with each round of replication. |
| telomerase | solves the problem of shortening, RNA template, Rev trans act, lengthens by 6 nucleotides |
| transcription | is the duplication of the genetic code, transcription is the first step in putting the code to work, syn RNA from a DNA template |
| transcription occurs | from one strand of DNA antisense, Sense strand is the coding strand |
| translation | proteins are made |
| transcription fact | All RNAs are synthesized from DNA; however, most of the DNA genome is dedicated to the synthesis of mRNA |
| Messenger (m)RNA | encodes the genetic information in the form of codons for direct synthesis of a polypeptide. |
| Reading frame- | sequence of codons for a specific protein |
| codons | encodes methionine, have redundancy in the third position |
| Prokaryote mRNA | polycistronic, Translation of mRNA can occur before transcription is complete. Messenger RNA is quickly degraded, lasting only a few minutes |
| Eu mRNA | transc and transl are separate, mRNA lasts for days, |
| Heterogenous nuclear RNA | also called the primary transcript, contains introns (non-coding intervening sequences) and exons (expressed sequences). |
| Alternative Splicing | Post-transcriptional modification is needed to remove introns, splice exons, and stabilize the mRNA |
| tRNA | transfers amino acids from the cytoplasm to the ribosome where a polypeptide is being syn, amino acid is attached to the 3΄-acceptor stem by aminoacyl-tRNA synthetase |
| rRNA | forms a functional ribosome. Important in the 3-D structure ribosomes, positioning mRNAs on the ribosome, initiate protein synthesis and have transpeptidase activity |
| Prokaryote (and organelle) ribosomes | 70S) have 23S and 5S rRNA in the large (50S) ribosomal subunit and 16S rRNA in the small (30S). |
| Eukaryote ribosomes | have 28S, 5S and 5.8S in the large subunit (60S) and 18S in the small subunit (40S). |
| Promoters | transc, Synthesis of RNA begins at a promoter site on only one of the two DNA strands to which the DNA dependent RNA polymerase binds. consensus seq |
| consensus seq promoters | Bacteria-Pribnow box located ten bases (-10) before the point of transcription initiation and the second sequence -35 Archea and Eu- -25 |
| Transc:Initiation | requires the binding of factors to DNA or the RNA polymerases. |
| Transcription:Ini, Bac | sigma factor () joins the core enzyme to form a holoenzyme for preferential transcription of genes. Different sigma factors exist for transcription of different genes. |
| Transcription:Ini, Eu, Arc | Initiation of transcription requires binding of transcription factors (TF) such as TATA-box binding factor to DNA, additional binding factors and the polymerase. |
| DNA dependent RNA polymerase | Bacteria have 1 RNA plms. Eu have 4 types of RNA plms, 3 in nucleus syn dif RNA. Type I syn rRNA , type II syn mRNA, and type III syn tRNA and 5S rRNA. Archaea possess one type of RNA polymerase most similar to type II of eukaryotes |
| Trans: Elongation 1 | The RNA polymerase moves down the DNA template in a 3’ to 5’ direction while the RNA is synthesized 5’ to 3’. The first base that signals transcription is usually a purine (A or G). |
| Trans: Elongation 2 | Approximately 10 bases down the sigma factor (prokaryote) or transcription factors (eukaryote) is/are released and free to associate with another RNA polymerase, leaving a core RNA polymerase to complete transcription. |
| Transc: Termination Pro | mRNA transcript to fold back on itself to form a stem and loop structure. The polymerase stops transcribing and dissociates at the poly-U or when an additional factor, the rho () factor causes the transcriptional complex to dissociate |
| Transc: Termination Eukaryotes: | Poly-T and poly-A, Termination of transcription is not well understood. One sequence that is invariant in eukaryote mRNA is the sequence 5'-AAUAAA-3' |
| Transc: Termination Arc | Poly-T region on the DNA template is implicated in contributing to termination |
| Post trans mod | in the eukaryote is further modified by capping, tailing, and splicing in the nucleus to form mRNA, and then transported to the cytoplasm where it can be translated by ribosomes |
| Splicing | introns removed by spliceosome (Type II introns) or ribozyme activity (Type I) and exons joined. Alternative splicing |
| Capping | The 5΄ end of the mRNA is capped, or blocked, by adding 7-methylguanosine to assist in recognition of mRNA by the small ribosome unit |
| Tailing | removing a small piece of the mRNA by endonuclease. The tail is added to increase the stability of mRNA and protect it from exonuclease digestion and possibly aid in translation. |
| Translation | Proteins are synthesized during translation by a three-step process that begins with initiation, progresses through elongation, and ends with termination. Occurs in Rib.2 ATP and 3 GTP |
| Translation: Initiation | Translation begins with the formation of an initiation complex made up of mRNA, initiator-tRNA, ribosome and initiation factors, GTP |
| Transl: Elong | has three sites for tRNA occupancy, the A (amino acyl, or acceptor) site, the P (peptidyl, or donor) site and the E (empty) site |
| Transl: Rlong 2 | N(amine)to C(carboxilic, E-spent, P-peptidyl binding site, A-holds growing chain, |
| Transl: Termination | protein synthesis occurs when the ribosome reaches one of three termination (nonsense) codons (UAA, UGA, or UAG). only 10 to 20 seconds to synthesize |
| release factors (RF-1,2,3) | bind to the ribosome, resulting in the release of the peptide from the final tRNA and dissociation of the ribosome |
| Inteins and exteinsq | removed, added to activate |
| Majority of proteins are secreted through the cell membrane | general secretory translocation pathway (Sec) or twin arginine translocation pathway (Tat). |
| translocons | Membrane transport complexes located in the membrane are called |
| Sec translocon | found in eukaryotes and prokaryotes. Proteins are guided to the Sec translocon by a protein chaperone (Sec pathway) or a signal recognition particle (SRP pathway) |
| Twin-arginine translocation (Tat | in contrast to Sec-dependent export, transports fully folded proteins across the membrane |
| Type I Protein Secretion Pathway or ABC Protein Secretion Pathway | common to all prokaryotes. various molecules including ions, drugs, and various sized (20-100 kDa) proteins such as hemolysin, proteases and lipases |
| Type III protein secretion pathways | are similar to the structure of the bacterial flagellum basal body. Acts like a molecular syringe through which a bacterium can inject proteins into eukaryotic cells. injectisome animal and plant pathogens |
| Type IV protein secretion pathways | homologous to conjugation machinery of bacteria (and archaeal flagella). capable of transporting both DNA and proteins. similar injectisome structure as Type III |
| Type II Protein Secretion Pathway Proteins: | In periplasm, a protein complex recognizes the and modifies the pre-proteins (cleaves signal sequence and folding modifications). Proteins are then transported through the outer membrane by a secreton. |
| Type V protein secretion pathways: autotransporter pw | are proteins are defined by the ability to drive their own secretion across the bacterial outer membrane . |
Created by:
wfetner
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