Introduction to Molecular Biology PDF

 introduction unit 1: to molecular biology Jo A the...

 introduction unit 1: to molecular biology Jo A the study of gene structure and function at the definition molecular level *What is a gene ? Chemistry ↳ : · which cellular chemicals is it made from ? ↳ genetics : · what does it do ? ↳ physics : What of · are the thermodynamics it ? * chemical components of the nucleac acid ↳ nitrogenous bases : : · purine > - adenine > - guanine · pyrimidine : > - cytosine > - thyamine > - uracil ↳ phosphoric acid : H - PO4 ↳ pentoses : · ribose · deoxyribose What * are nucleosides ? ↳ they are glycoside bonds between the nitrogenous bases and the pentose * where do these bonds form ? ↳ between the hydroxyl group at Cl of the pentose and the hydrogen H1 or 19 is a DNA molecule * why acidic ? ↳ due to the phosphate group A how does a DNA molecule become acidic ? ↳ phosphate associate becomes with release ofH ↓ and negativly charged to separate or break apart into elements A phosphodiester bonds ↳ bonds that form between two nucleotides * how are these bonds formed ? ↳ form between carbon at positions of one suger and the carbon at position 5' of the next suger A properties of double helix Complementar ↳ ↳ antiparallel ↳ helicoidal * what holds complementary strands togather ? ↳ energy of the hydrogen bonds * helicoida ↳ 2 strands that are not parallel but intertwined with eachother > - looks like helix ↳ double helix structure > - discovered by Watson and crick  * three different forms of double helix > - form A : when the amount of H20 is about 75 % 3) - form B : when the amount of H20 is about 92% > - form 2 : G - C (guanine - cytosine) rich regions > - hybrid RNA-DNA : has A form * hyperchrom ↳ DNA + RNA absorb UV at wavelength 200 nm ↳ Spectophotometer absorbs the wavelengths ↳ to find the concentration the absorbance has to be : · Single Strand DNA (SSDNA) > - X 40 · double strand DNA (dSDNA) - X50 * why does SSDNA absorb moreUV than as DNA ? ↳ because of DNA's hyprchromic affect which means that it happens because when denaturing we are adding an interway to absorb more * temprature of the fusion (TM) -> called melting point & the Tr of a given DNA sequance will correspond to the tempreture at which 50 % of the DNA is single strand ↳ the other 50 % is double strand im = 4x(GC] + 2x[AT]  the of different ? Why * is percentage Gandc slightly ↳ the present the more G and C higher the melting Point ↳ the average Ge content of a given DNA molecule can be determined from the point of this molecule melting * reassociation Kinetic types of first to DNA regions - associate & - ↓ gets associated when it is below Im > - melting point * where does DNA get denatured ? ↳ DNA denatured the start can be at any part not just on or end A-T rich first then G-C * regions separate and the region * what is nucleic acid hybridization ? ↳ creating a hybrid new from 2 diffrent DNA or RNA strands ↳ DNA replication and transcription needs to be tempoverly separated of the 2 strands ↳ separation is catalyzed by diffrent enzymic activities ↳ the 2 strands can be separated chemically by basic solutions like NaOH decreased * what happens when temprature is progressively ? ↳ the double helix will form again this is called hybridization * creating DNA-RNA hybrid * where can hybridization occur ? ↳ in solution ↳ on solid Support · bacteria colonies · chromosomes and tissue sections  unicellular organisms ↑ - unit 2 : transcription in prokaryotes * process : transcription * DNA-RNA- > protein Fanslation ↑ * * transcriptional ↳ bacteria is · what means environmental that do a they control stingy it doesn't change - do ? > organism transcribe when it doesn't turn genes on/off > - need proteins deal to energy saving with new environment * what makes bacteria transcribe ? ↳ environmental change because it depends or their need genes turned and off ? * why are on ↳ express when needed genes when not ↳ repress genes needed ↳ conserve energy recources & avoid expressing unnecercary genes transcriptional control processes A transcription A processing * translation ↳ initiation ↳ ↳ protein capping ↳ elongation ↳ splicing processing ↳ termination ↳ polydenylation ↳ turnover * operons groups of related transcribed by the promoter ↳ genes same in special cases ↳ , a group of genes can be controlled by one promoter m small peice of DNA upstream the gene that contains information on how to control said gene * what does transcription in prokaryotes usually has other than operons ? ↳ polysistronic RNAS- transcribed from operon - ↓ RNA that has many information from the genes controlled by 1 operon ↳ multiple genes transcribed as one transcript ↳ no nucleas so transcription and translation can occur simultaneosly * of RNA types RNA- mRNA ↳ messenger genes that encode protein · ↳ ribosomal RNA-rRNA · enzyme translated and in ribosomes stay · never · form the core of ribosomes ↳ transfer RNA-tRNA · adaptors that translation bring amino acids to mRNA during * RNA Synthasis transcription : ↳ RNAP binds to promoter emplate strand then opens and it b the strand that the read enzymes ↳ of RNA is also called closed complex binding polymerase a ↳ nucleosides are then added on 5'-3 ↳ separation of DNA then happens and is called open complex & Strand is identical to RNA coding ↳ steps include initiation and elongation as well * prokaryotic transcription initiation ↳ RNA polymerase · a , a , B, B , o Is components ↳ bacteria enzyme is E Coli. D promoter DNA ↳ has RNAP binding sites ↳ operator repressor binding ↳ other transcriptional factor (TF) binding sites ↳ start of transcription at+ initiation complex * prokaryotic transcription ↳ RNAP - called core enzymes ↳ has 4 subunits I · alphabeta-core enzymes that can't recognize promoter · alpha obeta ↳ Sigma factor is what recognizes promoter ↳ core enzyme + Sigma factor = holo enzyme * prokaryotic promoters ↳ typically has 2 elements ↳ have-35 and -16 ↳ usually transcription start is downstream by -10 element * the up element It ↳ is an AT rich part present in some strong promoters ↳ interacts with c-terminal domain of RNAP subunits * what does the Sigma factor do with holoenzymes when it binds to promoter sequence * Sigma (U) Factor functions ↳ Sigma + RNAP > - Step 1 > - Step 2 Step 3 > - also called > - Step 4 > - steps isinitiation] means binding/melting > - stepf > - Step 7 ↳ conformational changes that make it recognize the undergoes promoter region * Sigma factors ↳ recognize promoter ↳ Stimulates of polymerase to promoter binding ↳ they have factors with the same functions as general transcription factors in eukaryotes ↳ melts it DNA making an open complex ↳ variety of them present in E Coli. and each one is specific for a group of specific genes ↳ number of Sigma factors in bacteria depends on the environment they are present/live in ↳ for expression from most promoters is needed b essential for cell growth in all conditions ↳ Other Sigma factors are essential for special events like : 54 · nitrogen regulation - > 32 response to heat shock - - · porulationtion by pretending to be asleep * how specific are some Sigma factors in E Coli. promoters ? ↳ very specific but has small differences & CeCCATNIN is the sequance recognized by promoter on -10 in 832 * what regulates sigma factors ? ↳ number of copies per cell ↳ anti Sigma factors ↳ levels of effecter molecules ↳ transcription factor * bacteria RNAP numbers When bacteria is at metabolism it is "log Phase" ↳ high in Sigma factor domains both bind to - 18 binds to -35 - - ↳ involved in inhibition * constitutive and it promoters not all genes are regulated they , are only b genes that are regulated and are called regulated when they are needed houskeeping genes controlled by constitutive promoters ↳ inducible genes can be controlled life a light switch & transcription termination ↳ to stop the RNAP ↳ has 2 types · who independent : > - uses a structure of the RNA calledStem loop · who dependent : > - uses protein to catch up with RNAP and stop it > - like a race between RNAP and protein * Rho independent termination ↳ has 2 features : · Gerich self complimenting regions Series · of Uluracil) resides ↳ for the stem loop structure , as it is made the RNA is also being made * who independent steps GC rich make stem sequences bind to loop 2 stem loop causes RNAP to Stop 3 that with A DNA makes it unstable thus residues pair in releasing the RNA chain * Rho dependent termination ↳a hexameric protein with RNA helicase A who dependent steps > - relativly rare who binds to Crich sequence called rhoutilization or rut site about 80 of RNA Segments 2 base around it wraps 3 Atpase activity in who moves along RNA until RNAP Site unwinds DNA/RNAhybrid "termination depends on who's ability to catch up with RNAP * transcriptional attenuation ↳ attenuator site is when RNAP chooses between continuing transcription and termination ↳ uses a secondary structure trpperono * genes controlled by 1 promoter ↳ blocked when present tryptophan is ↳ has for base 4 regions pairing regions codes can b form For secondary structure amino acid ↳ Hyptophan is an amino acid made by bacteria * what makes each region form ? ↳ if the bacteria has a lot of tryptophan-region 3 and 4 are produced - ↳ if the bacteria has less tryptophan 2 and 3 are produced > - region What * do each region do ? ↳ region 2 and 3 · form Secondary structure · RNA polymeraze continuous transcription ↳ region 3 and 4 form structure · secondary · RNA polymeraze stops transcription