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Biology (Sci)
BIOL 200
Thomas Bureau

Lecture 1: Chemical Foundations - life occurs in a watery environment o biomolecules can be classified as hydrophilic (sugars), hydrophobic (fat), and amphipathic (phospholipids) - covalent bonds: strong bonds, small distance between atoms o carbon: most important atom, can form 4 covalent bonds o ie methane (tetrahedral), formaldehyde - noncovalent interactions: weaker, larger distance - common functional groups biomolecules: hydroxyl, acyl, carbony, carboxyl, sulfhydryl, amino, phosphate, pyrophosphate - common linkages: ester, ether, amide - polar bonds: O-H, C-O, N-H, P-O b/c of electric dipole moment - in water, covalent bonds >> noncovalent interactions; c-c bonds are especially strong - a single noncovalent interaction is unstable at biological temperatures; however, in a biomolecule, it is additive and very stable - the hydrolysis of ATP phosphoanhydride bond is -7.3 kcal, which is stronger than some covalent bonds but less than C-C bonds Lecture 2 - Noncovalent interactions: ionic interactions, hydrogen bonds, van dar walls interactions o Ionic interactions; NaCl has strong interaction, dissolve happily in water because it forms HYDRATION SHELL; for close contact protein-protein, water needs to be excluded o Ion-channel protein/Tetrameric channel: mediates transport of K+ from inside to outside of cell; transmembrane protein; hydration shell give selectivity of ion K+ channels because potassium ion is bigger than Na+ ion. There are amino acid residues that come in contact with the ion with polar oxygen atoms that are spaced like a hydration shell o Hydrogen bonds: in liquid water, dynamic network of hydrogen bonds; solubility in water depends on its ability to form hydrogen bonds, ie methanol, methylamine, peptide group, ester group o Van der waals interactions: weak, result from transient dipoles; occur in all types of molecules; form only when atoms are very close o Hydrophobic effect: aggregated state of hydrophobic molecules; hydrophobic surface area exposed to water is reduced; water population less ordered, higher entropy, energetically more favorable o Specificity of association between biological macromolecules is based on multiple noncovalent interactions precisely spatially organized Building Macromolecules - Monomers to polymers: amino acids  polypeptide (peptide bond for protein); nucleotide  nucleic acid (phosphodiester bond); monosaccharide  polysaccharide (glycosidic bond); in each case, when addition of monomer, molecule of water is released; all covalent bonds - Large structures based on noncovalent bonds: cytoskeleton o Actin filament, microtubule: Non-covalent bonds are easy to form and undo, thus the polymers are very dynamic o Lipid membrane: hydrophobic environment in the leaf (inside), hydrogen bonds & ionic interactions at exterior of membrane - Building blocks: amino acids o Base + acid = amphoteric o Alpha carbon atom that makes 4 covalent bonds o Hydrogen bond o Carboxy group COO- and amino group NH3+, make up backbone of protein, peptide bond with each other o R side chain: R group; 20 different amino acids, so 20 different R group; governs what kind of noncovalent interactions the proteins participate in o Hydrophobic amino acids: R groups with no polar bonds, except for tyrosine and tryptophan; alanine (Ala or A), valine (Val or V), Isoleucine (Ile or I), Leucine (Leu or L), Methionine (Met or M), Phenylalanine (Phe or F), Tyrosine (Tyr or Y), Tryptophan (Trp or W)  Aromatic rings are free to rotate  Hydroxyl group of tyrosine can be modified by phosphorylation (altered to phosphate group, highly charged, activates or inactivates protein) o Hydrophilic amino acids:  Basic: lysine (Lys or K, moderate), arginine (Arg or R, strong), Histidine (His or H, weak)  Acidic: Aspartate (Asp or D), Glutamate (Glu or E)  Polar amino acids with uncharged R groups: Serine (Ser or S), Threonine (Thr or T), Asparagine (Asn or N), Glutamine (Gln or Q) o “special” amino acids: cysteine (Cys or C, SH linkage and can form covalent interactions w/ other cysteine residues with disulfate bridge, important in conferring 2ndary structure), glycine (Gly or G, small and fits into tight spaces), proline (Pro or P, side chain links also to amino group in backbone, so they kink polypeptide group because of rigid bond, fixed angle) Lecture 3 - Cysteine: can disulfide bridge, covalent bond in extracellular space ie plasma, oxidizing ambient; in cytoplasm not bonded, so reducing ambient - Building blocks: sugars, from carbohydrate monomers (some multiple of CH2O) o Chemical groups: many OH + aldehyde or ketone o Glucose: terminal aldehyde group, asymmetric hydroxyl groups that form many different stereoisomers o Large variety of geometries high specificity of interactions o Proteins & nucleic acids polymerize in linear chain, but sugars branch Structure of nucleic acids - Slide 1: lampbrush chromosome o Site of RNA synthesis - Nucleic acids o DNA: contains all information required to build cells & tissues of an organism  Information stored in units called genes o Transcription: process by which information stored in DNA is copied into RNA for eventual use  2 kinds of genes: one is a gene that encodes RNA and then encodes protein; another class are noncoding RNAs that do not encode protein, but encode other things, ie ribosomal RNAs o Translation: process by which that information is used to create a protein of specific amino acid sequence - Molecular genetic processes and where they occur in the cell o Nucleus: where chromosomes of DNA is located; transcription, RNA processing, replication, place of DNA virus attack o Nucleolus: site of synthesis of rRNA o Cytoplasm: translation (ribosomes, amino acids, tRNAs, translation factors), attacked by RNA virus - DNA and RNA are linear polymers of monomers called nucleotides; there are 5 different nucleotides o Purines: adenine, guanine; aromatic ring that involves 9 atoms o Pyrimidines: cytosine, thymine (DNA), uracil (RNA), aromatic ring that involves 6 atoms o Phosphodiester linkage links 3’ hydroxyl group to 5’ hydroxyl group: sugar phosphate backbone o Most RNAs have <100 to 10,000 nucleotides o Cellular DNA molecules can be 100,000,000 nucleotides long o 5’ end has free phosphate group (attached to 5’ carbon) o 3’ end has free hydroxyl group (attached to 3’ carbon) o Polymer has inherent polarity and is directional o In DNA, double helix forms through hydrogen bonds between various functional groups of nucleotide bases; ie thymine has keto group and amine group which are polar, and can interact with amine; similarly, guanine has 3 groups than can base pair with cytosine o In artificial DNA, G-T and C-T base pairs fit within double helix o G-U base pairs quite commonly exist in double-helical regions of otherwise single-stranded RNA Lecture 4 - Bending DNA o DNA is flexible about its long axis because there are no hydrogen bonds parallel to the long axis o DNA binding proteins can bend DNA o DNA bending is necessary for it to be packed in chromatin - TATA box-binding protein: transcription of most eukaryotic genes requires TBP binding to their promoters; interacts with sequence of DNA and bends the DNA to pop chain apart and make bases accessible - DNA can undergo reversible strand separation o Single-stranded DNA absorbs more UV light than double-stranded DNA; temperature at inflection point of curve is Tm, melting point of double-stranded DNA o Tm shows percentage of G-C pairs: higher Tm means more G-C base pairs because G-C base pairs stabilize double-stranded DNA - DNA denaturation and renaturation o Denaturation of dsDNA: raise temperature, reduce ionic concentration, extremes of pH, add agents that destabilize hydrogen bonds (formamide or urea) o ssDNA can renature into dsDNA when these conditions are reversed; renaturation will only happen when ssDNA strands have complementary sequence; these experiments are nucleic acid hybridization - circular DNA molecules occur in prokaryotes and viruses o supercoiled or relaxed circle; topoisomerase I breaks 1 phosphodiester bond to turn supercoiled into circle - most RNA is single-stranded, but regions can base-pair to form specific structures thus can take many different shapes o secondary structure: hairpin, stem-loop (double-helical stem region) o tertiary structure: pseudoknot: 2 stem loop structures Transcription and mRNA Formation - Over view of transcription o DNA double helix locally denatures and one strand acts as a template for RNA o Incoming ribonucleotide triphosphates base-pair with bases in the template DNA strand o RNA polymerase sequentially joins rNTPs from 5’ to 3’ by forming phosphodiester bonds  Polymerization energetically favored because high-energy bond between alpha and beta phosphates is replaced by lower energy phosphodiester bond o 3 stages of transcription  Initiation: polymerase binds to the promoter sequence (denotes start of gene), locally denatures the DNA, and catalyzes the first phosphodiester linkage  Elongation: polymerase advances 3’  5’ down the template strand, denaturing the DNA and polymerizing the RNA  Termination: polymerase recognizes a stop site, releases the complete RNA and dissociates from DNA Lecture 5 - Transcription initiation o RNA polymerase (big) binds to promoter sequence in duplex DNA; start site near 3’ end, stop site further along; this is called the CLOSED COMPLEX because DNA is not yet denatured  Eukaryotic RNA polymerases require associated proteins called general transcription factors to find promoters and initiate transcription o Polymerase melts duplex DNA near transcription start site, forming a transcription bubble that is about 14 base pairs, allows rNTPs to begin RNA synthesis; OPEN complex o Polymerase catalyzes phoshosphodiester linkage of 2 initial rNTPs - Transcription elongation o Polymerase advances 3’  5’ down template strand, melting duplex DNA and adding rNTPs to growing RNA; within bubble there is DNA-RNA hybrid region; nascent RNA, the chain being synthesized, comes off o Multiple polymerase molecules can transcribe the same template DNA strand at the same time o Elongation complex is very stable; polymerase does not fall off until it reaches the stop site o Speed of elongation around 1000 nt/min, so small genes are transcribed in a few minutes but big genes (with big introns) can take hours - Transcription termination o At transcription stop site, polymerase releases completed RNA and dissociates from DNA o Primary transcript: completed RNA molecule (mRNA not directly synthesized from DNA) o A specific sequence in the template DNA signals the bound RNA polymerase to terminate transcription - Image 1: E. coli RNA polymerase has 5 subunits; in diagram, DNA bends sharply upon entering the enzyme; inflection site is around the transcription start site, favors local denaturation - Organization of genes is different in prokaryotes and eukaryotes o Prokaryotic genome is very compact; genes with a common function are often arranged linearly in operons & transcribed together on a single mRNA; there are very few non-coding gaps of DNA in prokaryotic genomes (no introns, no RNA processing) o Eukaryotic genome such as in yeast have genes scattered on several chromosomes; that means that coregulation is not achieved simply by physical linkage o In prokaryotes, mRNAs are directly transcribed from DNA; but in eukaryotes, transcripts must go through several processing steps before becoming mRNAs - RNA processing o As the 5’ end of a nascent RNA chain emerges from RNA polymerase, the 5’ cap structure (7- methyl-G) is added to it by several enzymes (5’ to 5’ linkage) o Polyadenylation: addition of 100 to 250 A residues by poly(A) polymerase on 3’ end of mRNA enzymatically o Intron excision, exon ligation (first exon will always include 5’ UTR, last exon will always include 3’ UTR) o mRNAs retain untranslated regions (UTRs) at the 5’ and 3’ ends but they do not encode for proteins; UTRs contain elements that regulate translation of mRNA & recruit ribosome to RNA o open reading frame: part of the RNA that encodes for the protein o the same primary transcript can be alternatively spliced in different tissues; liver cells remove exons EIIIB and EIIIA, while fibroblasts retain them; these cell types would then produce different forms of the protein encoded by this gene; alternative splicing increases protein diversity - in eukaryotes, elements that regulate transcription of a gene can span many kilobases o RNA polymerase binds to a promoter element o However, transcripton factors that regulate expression of a gene can bind to regulatory sites that can be tens of kb upstream (opposite to direction of transcription), or downstream of the promoter (very distant and still able to regulate) - 3 eukaryotic RNA polymerases o RNA polymerase I: located in nucleolus, transcribes only precursor ribosomal RNA (present in structures that look like prokaryotic operons) o RNA polymerase II: transcribes mRNAs and four small nuclear RNAs that take part in RNA splicing o RNA polymerase III: transcribes tRNA, 5S rRNA, and other small stable RNAs including one involved in RNA splicing Lecture 6 - Image 1: RNA polymerase II: examine in bacteria and yeast a) bacterial RNA polymerase II: 5 subunits, β, β’, αI, αII, ω b) yeast RNA polymerase II: 12 subunits, RPB2, RPB1, 3, 11, 6, & additional enzyme-specific subunits - largest subunit of RNAP II has a carboxy-terminal domain CTD (not in prokaryotes) o in mammals, CTD made up of 52 nearly identical repeats of Tyr-Ser-Pro-Thr-Ser-Pro-Ser; these amino acids have hydroxyl groups that can be post-translationally modified into a phosphate group (phosphorylated); because of Proline, the structure is also rigid o RNA polymerase molecules that initiate transcription have an unphosphorylated CTD o RNA polymerase molecules that are actively transcribing (elongation) have phosphorylated CTD - transcription initiation: requires formation of pre-initiation complex o pre-initiation complex contains many general transcription factors (TFII for factors associated with RNA polymerase II) in addition to RNA polymerase; required for transcription of ALL RNA polymerase-dependent genes o first step of transcription initiation: TATA-box binding protein TBP binds to TATA box of DNA  in vivo, TBP is part of TFIID, a complex of TBP and 13 other subunits called TBP- associated factors TAFs  TFIIA also required in vivo; it forms a complex with TFIID and TATA box  Recognition of TATA box also bends the DNA o TBP binding is required for TFIIB to bind; it binds to both DNA and TBP; does not have to be sequence specific because binding is cooperative and TBP can guide it to correct sequence on DNA o Next, RNA Pol II is recruited to pre-initiation complex with TFIIF (tetramer) with CTD sticking out at the carboxyl end of Pol II o Transcriptional start site will be downstream from TATA box; distance defined as difference between where TBP and Pol II binds o TFIIE (tetramer) binds next o TFIIH (9 subunits)recruitment completes the pre-initiation complex  TFIIH is a helicase which locally unwinds DNA and allows Pol II to form the open complex  Another subunit of TFIIH is a kinase that phosphorylates CTD, promoting elongation o TFIIA: associated to promoter at same time as TFIID o As elongation starts, all general factors EXCEPT TBP is released  TBP stays so that another initiation complex can assemble rapidly Regulation of Prokaryotic Gene Expression - transcriptional control o usually the major mechanism for controlling production of the protein encoded by a given gene o transcription of a gene can be repressed (little or no mRNA is synthesized) or activated (up to 1000x + mRNA is synthesized) - operons o about half the genes in E. coli are organized into operons o operons group genes that are in the same functional pathway o the lac operon encodes 3 enzymes required for catabolism of lactose; lactose activates lac operon o the trp operon encodes 5 enzymes required for biosynthesis of tryptophan; lack of tryptophan activates trp operon o transcription of operons and isolated genes controlled by interplay between RNA polymerase and specific repressor and activator proteins (also exist in eukaryotic cells) o to initiate transcription, E. coli RNA polymerase must associate with a sigma factor (protein that recognizes promoter sequence), most commonly σ70 70  promoter is where σ binds, and therefore where RNA polymerase binds; promoters similar to consensus sequence are stronger  operator sequence is a control element that lac repressor binds when not bound to lactose, and blocks start site; prevents RNA polymerase from moving forward, or by steric hindrance  transcription is repressed when lactose is absent; when lactose is present, it binds to lac repressor, changing its conformation and releasing it from the operator sequence; transcription is de-repressed; lactose is therefore an inducer Lecture 7 o Activation (not de-repression) of lac operon transcription  low transcription of lactose because of existence of glucose; if glucose levels are low, then activated  E. coli synthesizes cyclic AMP in response to low glucose levels  cAMP binds to, and makes active, a transcriptional activator protein called CAP (see image I)  CAP binds to CAP site when complexed with cAMP  CAP-cAMP interacts with RNAP and greatly stimulates rate of transcription initiation o Sigma factors  Recognize specific DNA sequences as promoters and recruit RNA polymerase  σ is best known, recognizes TTGACA….TATAAT (consensus sequence)  σ recognizes promoters of genes involved in nitrogen metabolism; the consensus sequence is very different; genes with σ promoters are also regulated by enhancers 80- 160 bp upstream that are activated by NtrC (DNA-binding protein), which in turn is activated by phosphorylation; this is similar to eukaryotic promoters because of longer range interactions - regulatory sequences in protein-coding genes o consensus sequence: where the nucleotides usually appear in TATA box positions o genes that are transcribed at high levels (have strong promoters) have a TATA box starting 35 bp upstream of the starting site; the TATA box functions similarly to an E. coli promoter, positioning RNA polymerase for transcription initiation - alternatives to the TATA box o some genes have an initiator element which includes a C at the -1 position and an A at the +1 position; no good consensus sequence has been defined o some genes initiate transcription at multiple sites within a 20-200 bp region; these genes lack a TATA box or an initiator element, but contain a CG-rich stretch of 20-50 bp (called CpG island) within ~100bp of the start-site region - promoter-proximal elements o in this course, the term promoter will be used for the TATA box or other sequences that recruits RNA polymerase to the transcription start site o promoter-proximal elements: other sequences near the promoter (100-200 bp) can regulate transcription o promoter-proximal elements can be cell type specific o ie control elements, detected by linker-scanning overlap mutations; good for a short stretch of DNA analysis; vector RNA can replicate in cultured cells; controlled region for detection, reporter gene is easy to measure, forms nontoxic product, and has no conflict with control region genes - in eukaryotes, elements that regulate transcription of a gene can span many kilobases o RNA polymerase binds to a promoter element o However, transcription factors that regulate expression of a gene can bind to regulatory sites that can be tens of kb upstream (opposite direction of transcription) or downstream of promoter o Deletion analysis can identify these elements: fragments cloned to vector, then vector fused to reporter genes; a nested series of deleted segments are made (nested deletion, look at reporter gene results) Lecture 8 Genomics - hox genes: set up body plans for developing embryos - Is most DNA “junk”? o C-value Paradox: genome size does not correlate with biological complexity o G-value paradox: number of protein-coding genes does not correlate with biological complexity o Things to consider: cis-regulation, alternative splicing, redundant genes, multi-functional (swiss- army knife proteins), post-translational modifications - DNA microarrays o Consists of thousands of individual, gene-specific DNA sequences attached to a glass slide or “gene chip” in a known array o Can be used to analyze global patterns of gene expression, in particular cell types, at particular stages of development, or in response to specific physiological changes o Isolate total mRNA, reverse-transcribe to cDNA labeled with fluorescent dye; shows genes expressed (green glucose-driven, red ethanol-driven) - genomics and evolution o in evolution, sometimes genes get duplicated, then each copy can diverge and take on slightly different functions; even whole genome duplication are possible o phylogenomics: take genomes of different organisms and compare o species-level genomics: compare tiny degrees of variation, ie of Drosophila o population genomics o genomic expansion: structural, functional, comparative, evolutionary, nutrigenomics, pharmacogenomics, synthetic genomics Lecture 9 - enhancers (eukaryotes) o can be >50 kb away from the genes they regulate o can be upstream from a promoter, downstream from a promoter, within an intron, or even downstream of the final exon of a gene (end of transcriptional unit) o are often cell type specific o image 1 experiment: transfection assay illustrates activity of SV40 enhancer; plasmic 2 has only the β-globin gene, plasmid 1 has both the β-globin gene and the SV40 enhancer; much more β- globin mRNA is synthesized by cells containing plasmic 1  steps: transfect plasmid 1 or 2 into cultured fibroblasts; isolate RNA and hybridize with labeled β-globin DNA probe; treat with S1 nuclease (does not effect double-stranded DNA) and then denature; perform gel electrophoresis and autoradiography - most eukaryotic genes are regulated by multiple transcriptional control elements o distinction between promoter-proximal elements and enhancers is unclear; a spectrum of different elements can regulate genes from different distances o many yeast genes have a regulatory element called UAS (upstream activating sequence) that works like an enhancer; in yeast the TATA box is about 90 bp upstream from the start site - activators and repressors of transcription o transcriptional control elements like enhancers are binding sites for regulatory proteins (transcriptional factors) o these proteins can be identified by biochemical techniques: DNase I footprinting, Electrophoretic mobility shift assay EMSA (or gel shift) - DNase I footprinting experiment: reveal specific binding sites for DNA binding proteins o Logic: if a protein is bound to a specific DNA sequence, then it can protect that sequence from nuclease digestion o DNA is end-labelled at 5’ end and partially digested with a nuclease that cuts randomly; a low concentration will chomp randomly within the sequence, then spread on gel from 100-1; when DNA binding is stuck on DNA, at certain positions of DNA, the nuclease will not cut; the blindspot not cut is the FOOTPRINT - EMSA or gel shift assay: used to detect DNA binding proteins during biochemical purification; if a DNA molecule migrates at a certain base in a gel, a protein bound to it will move slowly, so its spot on the gel will shift; gives assay for DNA purification o Better than footprinting for quantitative analysis of DNA-binding proteins, but doesn’t provide the specific DNA-binding sequence o Logic: a segment of DNA bound to a protein will migrate slower in a gel than the DNA alone - Co-transfection assay: in cultured cells are used to evaluate whether a protein encoded by a known gene is a transcription factor Transcription factors - transcription factors: proteins that stimulate or repress transcription for specific sets of genes, bind to promoter-proximal elements and enhancers in eukaryotic DNA - transcription factors are modular proteins containing a single DNA binding domain and one or more activation domains (for activators) or repression domains (for repressors) - purification of transcription factors o map the binding site (by footprinting experiments using nuclear extracts) o synthesize a DNA sequence containing multiple copies of the binding site and couple it to beads o incubate nuclear extract with the beads, wash, then elute proteins with increasing salt concentration; use EMSA to detect which factions have the DNA binding protein o test to see whether protein can stimulate transcription o image II: SP1 is a transcription factor that binds a segment of SV40 virus DNA and was purified; SP1 can greatly stimulate transcription from SV40 promoter, but has no effect on another viral promoter o co-transfection assay: most commonly used to evaluate potential transcription factors; these assays can identify repressors as well as activators o co-transfection assay production: one plasmid/lk has genes that produce a transcription factor; a second has a binding site and a reporter gene; now put both into cell Lecture 10 - transcriptional activators o activators are modular proteins that have distinct functional domains: DNA binding domain, activation domain, which interacts with other proteins to stimulate transcription o example: image 1, reporter-gene construct: UAS is an enhancer element that=binds a transcriptional activator called GAL4  deletion analysis of the GAL4 protein showed that the DNA-binding function could be separated from the transcriptional activation function o modular structure of different transcriptional activators: domain-swapping experiments also prove the modular nature of these proteins; if a DNA-binding site from one transcriptional activator is fused with the activation domain of another, a functional protein results - transcriptional repressors o functional converse of activators o most are modular proteins with a DNA-binding domain and a repression domain o like activation domains, repression domains function by interacting with other proteins - control regions often contain binding sites for multiple transcriptional activators and repressors o ie image 2: EGR-1 control region has WT1 repressor binding sites, SRF/TCF activator binding sites, and AP1 activator binding sites - types of DNA binding domains o zinc-finger motifs: C4 zinc finger; found in ~50 human transcription factors of the nuclear receptor family; these proteins generally contain only 2 such units but bind as homodimers (composed as 2 identical polypeptides); these have twofold rotational symmetry and bind to consensus DNA sequences that are inverted repeats  C2H2 zinc-finger protein, monomeric o Leucine-zipper: consensus has a leucine residue at every seventh position; bind DNA as dimers, often heterodimers; related proteins have a different repeated hydrophobic amino acid  Basic zipper bZip is term for larger family of proteins o Basic helix-loop-helix bHLH: similar to basic zipper except a nonhelical loop separates two α- helical regions; different bHLH proteins can form heterodimers - how can the finite set of transcription factors generate enough regulatory diversity? Increasing regulatory diversity o heterodimers: in some heterodimeric transcription factors, each monomer has different DNA- binding specificity; combinatorial possibilities increase diversity (3 monomers can make 6 dimers, 4 can make 10, etc) o inhibitory factors: can block DNA binding by some bZip and bHLH monomers o cooperative binding of unrelated transcription factors to near by sites (stimulating or blocking binding); ie image 3 AP1 (lucine zipper) and NFAT that bind cooperatively - activation domains o less sequence consensus than for DNA-binding domains o many activation domains have a high percentage of one or two particular amino acids (Asp, Glu, Gln, Pro, Ser, Thr) o acidic activation domains (those with Asp or Glu) are active when bound to a protein co- activator  eg 1: CREB must be phosphorylated to bind its co-activator CBP, which changes its conformation and makes an active transcription factor  eg 2: RARγ (retinoic acid receptor) has to bind retinoic acid to be in an active conformation o image 4: cooperative binding of multiple activators to nearby sites in an enhancer forms a multiprotein complex called enhanceosome, whose assembly often requires small proteins that bind to the minor groove and sharply bend the DNA  on the β-interferon enhancer  IRF-3 and IRF-7 are monomeric transcription factors; cJun/ATF-2 and p50/p65 are dimeric transcription factors; these all bind highly cooperatively; HMGI binds the minor groove of DNA regardless of sequence, thus bending the molecule and allowing the transcription factors to interact Post-transcriptional steps of gene expression - overview of eukaryotic mRNA processing: once primary transcript produced,
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