Week 12-14 Notes (Sorry for the wait guys!)
Week 12-14 Notes (Sorry for the wait guys!) Bio 1510
Popular in (LS) Bas Life Mch
verified elite notetaker
Popular in Biology
This 23 page Bundle was uploaded by Nausheen Zaman on Saturday December 12, 2015. The Bundle belongs to Bio 1510 at Wayne State University taught by Dr. Nataliya Turchyn in Summer 2015. Since its upload, it has received 72 views. For similar materials see (LS) Bas Life Mch in Biology at Wayne State University.
Reviews for Week 12-14 Notes (Sorry for the wait guys!)
Report this Material
What is Karma?
Karma is the currency of StudySoup.
You can buy or earn more Karma at anytime and redeem it for class notes, study guides, flashcards, and more!
Date Created: 12/12/15
Chapter 13 (con) ● If Two Alleles are on the Same Chromosomes, They can be Inherited Together ○ In paternal and maternal chromosome #10… ○ Gene X hair color ■ A = dominant allele ■ a = recessive allele ○ Gene Y eye color ■ B = dominant allele ■ b = recessive allele ○ Linked genes genes located on the same chromosome ■ Can be inherited together (like red hair and freckles) IF there is no crossing over ■ Causes parental gametes ● 4 gametes will be produced with unaffected chromosomes ● … But not Always ○ If crossing over occurs ■ Parental and recombinant gametes will be produced ■ Recombinant gametes gametes with new combo of alleles ○ Recombinant gametes for because of crossing over between genes X and Y ● Using Recombination to Measure Distance Between Genes ○ Gene X and Y located on same chromosome in Drosophila ■ + normal ■ vestigial wings = short wings ○ 415 mat phenotype ○ 405 pat phenotype ○ 92 matpat phenotype (gray vestigial) ○ 88 patmat phenotype (black normal) ■ Because of crossing over between wing size and body color genes (this gave rise to recombinant offspring) ○ Recombination frequency = recombination (translated into the distance between linked genes) ■ Wing size + body color are located 18 cMs aparts from each other on the same chromosome using formula ○ Crossing over most likely to happen when two genes are far apart from each other than when they are next to each other ○ ● Which Genes are Closer to Each Other? ○ If only crossing over event 1 (#1 in picture) occurs: aBC, Abc (2 crossing over events occur) ○ If only crossing over event 2 (#2 in picture) occurs: ABc, abC (2 crossing over events occur) ○ If both crossing over events 1 and 2 (cross over at #1 and then cross back over at #2) occur: AbC, aBc (2 events occur) Chapter 14: DNA The Genetic Material ● Review of Nucleotide structure ● Different Nitrogenous Bases ● How is DNA Synthesized? ○ Phosphodiester bond forms between 5’ phosphate groups of one sugar and 3’ OH (hydroxyl) group of adjacent sugar ○ Linear strands of DNA have a free 5’ phosphate group and free 3’ OH (hydroxyl) group ● 3D Structure of DNA ○ Rosalind Franklin and Maurice Wilkins ■ Xray diffraction studies suggested that DNA had helical shape of about 2 nanometers (nm) ○ James Watson and Francis Crick ■ Figured out DNA was a double helix ● 2 strands of nucleotides ● Bases point inwards to for base pairs ● Purines paired with Pyrimidines ■ Strands antiparallel ● One strand runs 5’ 3’ ● Opposite strand runs 3’ 5’ ● Base Pairing ○ Pyrimidines always pair with purines ○ T A bond = 2 H bonds ○ C G bond = 3 H bonds ● DNA Replication Semiconservative ○ Parent DNA molecule unzips ○ Each parent DNA strand = template for new daughter DNA strand ■ Confirmed by MeselsonStahl Experiment ● DNA Replication Process ○ Replication of DNA begins at several specific site along DNA molecule (origins of replication/replication origins) ○ DNA polymerase 3 works with other enzymes to generate DNA strands ○ Eukaryotes have many origins of replication ○ Prokaryotes only have ONE origin of replication ● Actions of DNA Polymerase 3 ○ DNA polymerase 3 moves along template strand’ → 5’ direction ■ Adds free nucleotidonly to a free 3’ OH of daughter strand ○ Daughter strandformed/synthesized 5’ → 3’ direction ○ Summary: ■ Always moves along daughter strand in a 3’ à 5’ direction (top to bottom end) ■ Creates phosphodiester bond ■ When template strand sees unpaired T, pairs a freefloating A to complete strand (2H bond created) ● 3H bond created between C and G ■ Makes daughter strand from 5’ – 3’ direction ● DNA Replication Continues ○ DNA gyrase stops DNA from twisting ○ DNA helicase opens up helix (unzips your genes) ○ DNA polymerase 3 requires a primer (DNA primase, an RNA polymerase, constructs this primer) to which it adds first nucleotide ■ Adds nucleotides to 3’ end ■ Leading strand replicates towards replication fork ● Synthesized continuously (gets preferential treatment because of its leading status) ■ Lagging strand elongates from replication fork ● Synthesized discontinuously (doesn’t get preferential treatment because it lags all the time :() ● Production of Okazaki fragments occurs here ○ DNA polymerase 1 removes RNA and fills in gaps ○ DNA ligase attaches Okazaki fragments to lagging strand ● DNA Replication Fork ○ Leading and lagging strands → make daughter (leading and lagging) strands ○ Without SSB (singlestrand binding proteins), parents strands come back together ■ SSBs keep them apart ○ RNA Primer Facts ■ Complementary to DNA (means that nitro bases of RNA primer can form hydro bonds with nitro bases of DNA) ● A (RNA primer) = T (DNA) ● G (RNA primer) = C (DNA) ● U (RNA primer) = A (DNA) ■ RNA primer and DNA run antiparallel to each other (opposite directions ● DNA – 3’ → 5’ ends ● RNA Primer – 5’ → 3’ ends ■ Last ribonucleotide has a free 3’ OH to which DNA polymerase 3 can st attach to deoxyribonucleotide ● DNA Synthesis ○ Only one primer required to initiate and propagate leading daughter strand synthesis ■ Think of a domino effect for leading strand that is continuous ○ Leading daughter strand synthesized CONTINUOUSLY in 5’ → 3’ direction ○ Unlike the leading daughter strand… ■ The lagging daughter strand is synthesized DISCONTINUOUSLY in small segments ● These segments are called Okazaki fragments (only lagging daughter strands have them because they are problematic) ● Think of lagging daughter strand as a rusty car, Okazaki fragments are the pieces that keep falling out the car ■ Multiple RNA primers needed to synthesize lagging daughter strand ○ DNA polymerase 3 (true for all other polymerases) ALWAYS moves along leading and lagging parent strands in the 3’ → 5’ direction, makes leading and lagging daughter strands in the 5’ → 3’ direction ○ When DNA polymerase 3 encounters preceding primer, lifts lower arm ○ DNA polymerase 1 removes RNA primer, fills gaps between Okazaki fragments with deoxynucleotides ■ DNA polymerase 1 (prokaryotes) – very similar to DNA polymerase 3, can only add deoxynucleotides to a free 3’ OH of another nucleotide ■ DNA repair enzyme (eukaryotes) used instead of DNA polymerase 1 ○ DNA ligase joins Okazaki fragments together with phosphodiester bonds ■ Handyman of DNA synthesis ○ DNA polymerase 3 puts lower arm into a new location ○ DNA polymerase 3 synthesizes a new Okazaki fragment until it reaches previous RNA primer ● KNOW FOLLOWING PROBLEM AND HOW IT WORKS FOR THE EXAM! ● ● Why Do Chromosomes become Shorter? ○ 3’ end of lagging strand CANNOT be replicated ■ Overtime telomeres become shorter when cells are being divided ○ Telomeres become shorter because of DNA repair polymerase – similar to DNA polymerase 1 ○ Cannot replace last RNA primer of lagging daughter strand due to lack of nucleotides with a 3’ hydroxyl group (3’ OH) ○ Telomeres found in eukaryotes ● Telomerase: Keeping Telomeres Long Enough ○ Telomerase → reverse transcriptase → enzyme that reverses transcription ■ Transcription when DNA used to make RNA ■ Reverse transcription when RNA used to make DNA ○ Each linear chromosomes has two telomeres ● How Does Telomerase Work? ○ Reverse transcriptase – enzyme that uses RNA to make DNA (has its own RNA molecules) ○ Telomerase RNA is used to rebuild the telomere (a repetitive DNA sequence ie. TTGGGG) ○ Attaches unpaired nitro bases to telomerase RNA with Hbonds ○ Telomerase uses its RNA molecule as a template for rebuilding the telomere by adding deoxynucleotides to it ○ Remember C has 3 HBonds to G, A has 2 Hbonds to T ○ Telomere consists of deoxynucleotides and telomerases add deoxynucleotides to the telomere using RNA molecule inside as a template until it is long enough → DNA primase creates RNA primer → RNA primer’s last ribonucleotide has 3’ OH group where DNA polymerase can attach the first deoxynucleotide → DNA polymerase synthesizes lagging daughter strand in 3’ – 5’ direction, grow from 5’ – 3’ end ● How can DNA be Damaged? ○ In presence of UV light, adjacent T can create covalent bond with each other rather than Hbonds with A ○ Tdimer/Pyrimidine dimer causes DNA to be kinked ○ Kinked copy of DNA can cause mutations that lead to diseases like cancer if left unrepaired ○ Kinked uncorrected Tdimers can cause melanoma (skin cancer) in humans ● Photorepair ○ Also called photoreactivation repair – mechanism that uses a photolyase (an enzyme that repairs Tdimers, binds to Tdimers and breaks covalent bond in order for the AT Hydrobond to occur) to repair thymine dimers ○ Photolyase activated in visible blue light ○ Used by bacteria, fungi and plants to fix Tdimers, but not by humans ● Excision Repair ○ Used by humans to repair thymine dimers and incorrect/damaged nucleotides ○ Excision repair enzymes divided into 2 groups: ○ Exonucleases – cleave nucleotides from the ends of DNA/RNA ○ Endonucleases – cleave nucleotides in the middle of DNA/RNA ○ Singlestranded gap/break is created with endonucleases/ionizing radiation (Xrays and gamma rays) → DNA polymerase fills in the gap with missing deoxynucleotides using undamaged DNA strand as a template → DNA ligase seals nick left in sugarphosphate backbone of repaired DNA strand by creating a phosphodiester bonds ○ Photorepair uses one enzyme ○ Excision repair uses three enzymes ● The MeselsonStahl Experiment ○ E. Coli were grown in a heavy isotope of nitrogen, N15 ○ All DNA incorporated N15 ○ Cells were then switched to media containing lighter isotope of nitrogen N14 ○ DNA was extracted from the cells at various time intervals ○ DNA replication is semiconservative (every daughter DNA molecule always consists of one parent strand and one new strand) ○ E. Coli are prokaryotes ○ Gen 0 – E.coli whose DNA was labelled and immersed in 15N ○ Gen 1 – E.coli whose DNA was immersed in N15 and replicated in N14 ○ Gen 2 – E.coli whose DNA replicated in the N14 ○ Results… ■ Gen 0 – Heavy density molecules that produced a band at the bottom of the tube ■ Gen 1 – Labelled with both N14 and N15, of intermediate density and had a band in the middle of the tube ■ Gen 2 – Two band were formed; DNA labeled with N14 and N15 were of intermediate density, DNA labelled with N14 were of lighter density (the band at the top of the tube) ○ Concluded that during DNA replication, parent strands come apart and are used as a template for a daughter strand, making two new daughter DNA, and in Gen1 they have both characteristics of parent and new strand, and in Gen 2 there were characteristics of affected parent strand (N15) and unaffected parent strand (N14) ● Is Genetic Information in Protein or DNA? ○ Avery Experiment ■ Worked with bacteria that transferred genetic material between each other (transformation) ■ Removed almost all proteins from bacteria and found no reduction in transforming activity ■ Concluded that protein was not genetic material ● However, since he didn’t remove ALL genetic material some scientists doubted his results ○ HersheyChase Experiment ■ Used different radioactive isotopes to label DNA and proteins in bacteriophages (viruses that affect DNA) ■ New bacteriophage passed genetic information into host cell, which was then used to produce new viruses ■ Found material used to specify new generations of viruses were made of DNA ○ Avery Experiment – worked with HersheyChase and assisted them with bacterial studies of DNA (some bacteria mate – transformation) ○ HersheyChase Experiment – wanted to know whether gen info is stored in proteins or DNA ● The HersheyChase Experiment ○ Wanted to know what bacteriophages pass onto bacteria when they infect them (DNA/protein) ○ Used radioactive materials (S35) to label bacteriophage DNA and bacteriophage protein (P32) ○ Why sulfur? Proteins are made of amino acids, some amino acids have cystine/methionine in their structure and sulfur binds to the sulfur in cystine/methionine structures ○ Why phosphorous? DNA is constructed out of a sugarphosphate backbone, and deoxynucleotide contain phosphorous in their Pgroups so P binds to DNA ○ Bacterial pellet checked for radioactivity ○ 1 experiment – S35 was found in the liquid above the solid pellet nd ○ 2 experiment – P32 was found in the bacterial pellet ○ This suggested that DNA was the material that was passed into bacteria, concluding that DNA was genetic material transferred from bacteriophages to bacteria Chapter 15: Genes and How they Work ● Different Types of RNA ○ Ribosomal RNA (rRNA) ■ RNA found in ribosomes ○ Transfer RNA (tRNA) ■ Temporary link between amino acids and mRNA that is being translated ○ Messenger RNA (mRNA) ■ Actual template for amino acid assembly in polypeptide synthesis ○ Small nuclear RNA (snRNA) ■ Involved in mRNA processing ○ Signal Recognition Particle RNA (SRP RNA) ■ Needed for proteins produced in rough endoplasmic reticulum ● How Does Transcription Begin? ○ RNA Polymerase ■ Always in the 3’ → 5’ direction along DNA ● Transcribes only ONE of two DNA strands ● Template/antisense strand ● Nontranscribed strand = coding/sense strand ○ Same sequence as RNA except for T in place of U ■ RNA polymerase adds ribonucleotides to the 3’ end of growing RNA chain ■ Promoter is a region of DNA template strand where RNA polymerase binds and initiates transcription ● Promoter not transcribed into RNA ● TATA box (region of DNA consisting of A and T bases) in prokaryotes/eukaryotes ● Initiating Transcription in Eukaryotes ○ Transcription factors proteins that help RNA polymerase to locate promoter and initiate transcription ■ Each gene controlled by several transcription factors ● Transcription in Prokaryotes ○ RNA polymerase doesn’t need transcription factors to bind to the promoter ○ RNA polymerase uncoils the DNA and uses only one strand (template) to synthesize RNA ○ As RNA synthesis continues, RNA strand peels away from DNA template ● Terminating Transcription in Prokaryotes ○ Stop sequences (terminators) ■ Located at the end of gene ■ Cause phosphodiester bond formation to halt → RNA polymerase to release DNA → DNA rewinds ● Terminators are transcribed = GC hairpin loop followed by UUUU ● RNA Processing (Eukaryotes) ○ Before RNA can leave the nucleus, it must undergo certain modifications: ■ Addition of 5’ cap (phosphate removed, GTP added) ■ Addition of 3’ polyA tail (about 25 Adenine ribonucleotides) ○ Both protect RNA from degradation by ribonucleases ○ MOdification convert RNA → primary RNA transcript ● RNA Processing Continues ○ Primary RNA transcript CANNOT be used as a template for protein production ■ Additional modifications are made: ● introns (noncoding sequences) removed (since they don’t code any proteins what do you need them for?) ● exons (coding sequences) brought together (code for different proteins you need those to live!) ■ How is this achieved? ● snRNPs (small nuclear ribonucleoproteins) associate with proteins to form spliceosome ● Single primary RNA transcript can be spliced to different mRNA by inclusion of different mRNAs by inclusion of a different set of exons (alternative splicing) ○ Additional modifications convert primary RNA transcript → mRNA ● How Does the Spliceosome Work? ○ Consists of several small nuclear ribonucleoproteins (snRNPs/ SNURPS) ○ SnRNPs: ■ recognize exonintron boundaries and consist of proteins and small nuclear RNAs (snRNAs) ○ Mature mRNA can go to the cytoplasm to be translated ○ ONLY Bacteria have RNA polymerase, Eukaryotes have RNA polymerase 1, 2, 3 ○ RNA splicing... ■ occurs in the nucleus ■ Spliceosomes have snRNPs ■ each snRNP has different function in splicing ○ Steps: 1. snRNPs containing a snRNA and protein come together at the ends of an intron 2. Intron must conta GU a 5’ en,AG at th3’ end,and anA (Adenine) within thbranch site 3.U1 snRNP → 5’ end of intron 4.U2 snRNP → branch site 5.U4, U5, U6 snRNPs → 3’ and branch site 6. All snRNPs come together, splicing intron at 5’ and 3’ ends 7.’ end connects at ‘A site’, forms a lariat 8.U1,U4 snRNPs arereleased 9.U5,6 snRNPs hift positions 10. Exons connected and lariat, U2, U5, U6 are released together 11. Rest of the snRNPs dissociated from lariat, which eventually degrades ● The Genetic Code: the Connection between mRNA and Amino Acids ○ mRNA is a blueprint for polypeptides ○ How do ribosomes ‘read’ the mRNA and know what amino acids to link together to form polypeptide? ■ When ribosomes move along mRNA → they ‘read’ three ribonucleotides at a time in the 5’ → 3’ direction ■ This is called a reading frame ● A set of three ribonucleotides → codon ● One codon = one amino acid ■ Genetic code tells which codons code for each of the twenty amino acids ● Some amino acids are encoded by more than one codon ○ UUA/UUG = Leucine ○ 61 codons specify for 20 amino acids (some amino acids have only one codon to code them) ● Preparing for Translation ○ The appropriate amino acid must be attached to its tRNA molecule ■ Performed by aminoacyltRNA synthetase ○ tRNA has two important sites: ■ Accepting site ■ Anticodon ● Contains three ribonucleotides complementary to the mRNA codon ● Anticodoncodon pairing is antiparallel ○ tRNA anticodon ○ It is mRNA codon (not tRNA anticodon) that determines what amino acid will be attached to accepting site of tRNA ○ tRNA without amino acid is an uncharged/empty tRNA ○ Charged tRNA has amino acids attached to accepting site ● Formation of Initiation Complex ○ Initiation complex includes small ribosomal subunits, mRNA and tRNA (met) ○ mRNA binds to small ribosomal subunit along with proteins called initiation factors ○ tRNA^met binds to mRNA codon ○ Large subunit binds to small subunit+mRNA+tRNA^met, completing the initiation complex ○ Ribosome has three sites: ■ P site holds tRNA with a growing polypeptide chain ● Also where the first tRNA^met enters ■ A site where the rest of charged tRNAs first enter ■ E site where uncharged tRNAs exit ● Elongation: Peptide Bond Formation ○ Elongation factors proteins that help deliver appropriate charged tRNA → A site ○ Two amino acids (attached to tRNAs in A and P sites) form a peptide bond between each other ■ Catalyzed by peptidyl transferase of large ribosomal subunit ● Also breaks bond between polypeptide chain and tRNA in P site ● Elongation of Polypeptide ○ Amino acid attached to tRNA in P site is released from its tRNA molecule ○ Called ‘empty’/uncharged tRNA ○ Ribosome shifts down mRNA to the next codon (translocation) ■ Translocation refers to the movement of ribosomes in the 5’ → 3’ direction ■ tRNA in P site moves to E site from which it becomes ejected and tRNA in A site moves to P site ■ new tRNA is brought into A site ○ Steps: 1. Charged tRNA with anticodon matches mRNA codon @ A site with elongation factor (EFTu) 2. EFTu hydrolyzes GTP, dissociates from ribosome 3. Peptide bond formed between A site amino acid + growing chain in P site 4. Growing chain transferred to A site, tRNA in P site ‘empty’ 5. Ribosome translocation requires another EFTu + GTP hydrolysis 6. tRNA moves to P site à A site, next codon goes to A site, ‘empty’ tRNA to E site ● Termination of Translation ○ Termination a nonsense (stop) codon is encountered ■ UAA, UAG, UGA ○ Stop codons recognized by release factors ○ Occurs when ribosomes encounter one of the three STOP/nonsense codons (tells ribo to stop translating) ○ Release factor binds to stop codon → binds to mRNA → new polypeptide released from ribosome ● How are Proteins Synthesized by the RER? ○ Eukaryotes translation occurs in the cytoplasm and the RER (rough endoplasmic reticulum ○ Proteins made in the cytoplasm are delivered to the nucleus, mitochondria, chloroplast, peroxisomes and endoplasmic reticulum ○ Proteins made in the RER are secreted (exocytosis – active transport) from the cell (secretory proteins) ■ Some are embedded into cell membrane (plasma membranes) and internal membranes (in animal cells, all organelles have them except for ribosomes) (transmembrane proteins) ○ Signal is a short sequence of amino acids that directs ribosomes with a growing polypeptide chain to rough ER → signal recognized by sRP (consists of SRP RNA and proteins) → SRP binds to signal and to ribosomes and arrest elongation of poly chain → SRP binds to SRP receptor (docking) → protein channel opens → polypeptide chain is ejected into lumen and elongation continues inside lumen → protein synthesis is completed, protein folds with assistance of chaperones (makes them functional) → proteins become modified ○ Ribosomes stay out of RER as they are too big to pass through the protein channel ○ 3 functions of RER: ■ Protein synthesis ■ Folds proteins (lumen) ■ Converted to glycoproteins (lumens) → transported to Golgi for packaging and distribution ● Prokaryotes vs. Eukaryotes ○ Operon group of genes that are transcribed into mRNA at once because they share a promoter ○ Prokaryotes – bacteria and archaens (no introns in bacteria, some in archaens) ■ Bacteria have operons ○ Eukaryotes – all animal cells (some eukaryotes have operons) ■ Operons more common in prokaryotes than in eukaryotes ■ Most genes have their own promoters in Eukaryotes ○ Prokaryotes have polycistronic mRNA (poly – many, cistron – gene) – encodes two or more proteins ○ Eukaryotes have monocistronic mRNA (mono – one) – encodes only one protein ○ Prokaryotes – transcription and translation are coupled (possible because both occur in cytoplasm) ○ Eukaryotes – transcription and translation are spatially and temporally decoupled ■ 5’ cap in eukaryotes have two functions ● Protects mRNA from degradation from ribonucleases ● Needed for translation to happen ● Point mutation change of one base pair to another ○ Three types of point mutations: ■ Missense mutation codon change alters the amino acid encoded ■ Nonsense mutation changes a codon specifying an amino acid into a termination codon ● Both are dangerous because they alter the coding of a protein ■ Silent mutation alters codon but doesn’t result in a change in the amino acid ● Chromosomal Mutations ○ Deletion part of chromosome that is deleted (makes it shorter) ○ Duplication part of chromosome that is duplicated (makes it longer) ○ Inversion segment of chromosome is broken in two places, reversed and put back together ■ Normal and inverted chromosomes are of the same length, but the order of genes are not the same ○ Reciprocal translocation nonhomologous chromosomes exchange regions with each other creating two new chromosomes ■ Crossing over usually occurs between homologous chromosomes (mat and pat chromosomes 10), however with reciprocal translocation it occurs between nonhomologous chromosomes (mat chromosome 10 and pat chromosome 5) ■ Reciprocal translocation = two types of leukemia Chapter 16: Control of Gene Expression ● Prokaryotes regulate gene expression in response to changes in the immediate environment (e.g. food supply) ○ Many changes are reversible ● Eukaryotes regulate gene expression to maintain homeostasis (dynamic constancy of internal environment) throughout the whole organism, not just within an individual cell ○ Many changes are irreversible ● DNA Binding Regulatory Proteins ○ Gene expression is often controlled by regulatory proteins binding to DNA ■ regulatory proteins may block transcription by getting in the way of RNA polymerase or stimulate transcription by helping RNA polymerase locate promoter ■ regulatory proteins bind to specific DNA sequence in major grooves ■ regulatory proteins possess DNAbinding motifs ● DNA Binding Motifs ○ Regions of regulatory proteins which bind to DNA ○ The HelixTurnHelix Motif ■ Two adjacent alphahelices separated by turn of several amino acids ● One helix (recognition helix) fits in major groove, other lays against outside of DNA molecule ■ Most common motif ■ Alphahelices an example of a secondary protein structure (formed from Hydrogen bonds) ■ Only ONE helix (recognition helix) binds to major DNA groove ○ The Homeodomain Motif ■ Special class of helixturnhelix motifs ■ Found in proteins that bind to genes expressed during specific stages of development ● Intraembryonic (before birth)/postembryonic (postbirth) development ● Same as HTH EXCEPT it has extra alpha helix ○ The Zinc Finger Motif ■ Uses zinc atoms to coordinate DNA binding ● More zinc fingers = stronger bond between DNA and protein ■ Each zinc finger = one zinc atom, one alpha helix, one beta sheet ● Alpha helix/beta sheet = secondary protein structures made from hydrobonds and peptide bonds respectively) ■ Some Transcription Factors have one, some have several ■ TF shown has three zinc fingers + alpha helix of each finger binds to major groove of DNA ○ The Leucine Zipper Motif ■ Two leucinerich regions (blue rods) interact with each other, forming a zipper ● Region beyond the zipper form Yshaped structure that grips the DNA in scissorlike configuration ■ Without zipper, two alpha helices will not be able to bind to DNA ○ Similarities ■ All bind to major grooves of DNA ■ All have at least ONE alpha helix in structure ● Prokaryotic Regulation ○ Control of transcription initiation ○ Positive control increases frequency of initiation ■ activators specific TF that enhance binding of RNA polymerase → promoter ○ Negative control decreases frequency of initiation ■ repressors specific TF that bind to operators (DNA regulatory sites) to prevent/decrease initiation of transcription ○ Many genes in bacteria are found in operons under control of same promoter and transcribed as one unit ■ Lactose (lac) operon (Induction) ■ Tryptophan (trp) operon (Repression) ● Both are found in E. coli (gram negative bacteria) ■ Operons also found in eukaryotes but they are more common in prokaryotes (because they don’t have enough space in one chromosomes for promoters) ■ Lac and trp operons found in e. coli (gram negative) ■ When lac operon is expressed → enzymes necessary for transport and metabolism of lactose (milk sugar) → glucose and galactose are made ■ Bacteria regulate the changes in gene expression according to their external conditions ■ When lac ipresent – lac operonxpressed ■ When lac iabsent – lac operonot expressedand genes/enzymes are not produced ■ Bacteria don’t waste time and energy with producing enzymes and transporting something that is absent (induced in the presence of lactose – substrate) ● Induction when bacteria produce enzymes for a certain pathway in response to substrate ■ When trp iresent trp operon NOT expressed ■ When trp iabsent– trp opero expressed ● Repression Bacteria are capable of making enzymes, but they don’t until there is a need for it ● The Iac Operon in E.Coli ○ Consists of a promoter, operator and three genes (lacZ, lacY and lacA), which encode three enzymes that transport/metabolize lactose ○ Beta galactosidase (lacZ), permease (lacY), transacetylase (lacA) ○ Under control of a single promoter shared by three lac genes, transcribed together into single long mRNA (polycistronic) → translated by ribosomes → three proteins which act as enzymes ○ How is a single polycistronic mRNA able to produce three proteins? Has three start and stop codons within mRNA ○ RNA polymerase binds to promoter in bacteria, repressor binds to operator, DNA also has lacI gene (repressor protein and its own promoter) ○ Lac operon not only regulated by the repressor, but also the activator/CAP (binds to CAPbinding site) ● When Lactose is Absent… ○ lac Operon iegatively regulabyrepressorprotein ■ lac repressor (regulated by lacI gene) binds to operator to block transcription ■ Result: Enzymes needed to metabolize lactose are NOT produced ○ Lactose absent = nonfunctional lac operon ● When Lactose is Present… ○ An inducer molecule (allolactose) binds to repressor protein ○ Repressor can no longer bind to operator ■ Allolactose makes repressor go through a shape shift and make it nonfunctional ○ RNA polymerase is allowed to move forward and transcribe enzymes for lactose metabolism ● When Glucose is Low and Lactose is Present… ○ lac operon positively regulateby an activator/catabolite activator protein (CAP) ○ cAMP binds to CAP → forming CAPcAMP complex → binds to CAP binding DNA site → bends DNA ■ DNA bending is important! Bending make RNA polymerase more efficient in binding to the promoter ○ In this state, lac operon achieves maximum level of expression for RNA polymerase and promoter
Are you sure you want to buy this material for
You're already Subscribed!
Looks like you've already subscribed to StudySoup, you won't need to purchase another subscription to get this material. To access this material simply click 'View Full Document'