Central Dogma: proposed by Francis crick, one information has got into Hereditary: tendency of an organism to possess the characteristics of DNA Polymerase I is not the replicative polymerase: Enzyme is too slow. Pol 1 Overview: DNA strands separate at origin of replication creating 2 replication
a protein it cant get out again. DNA -> RNA -> Protein. Genetic diversity: its parents. catalyzes the incorporation of dNTPs at maximal rate ~20 nt/sec. At this rate, strand replication proceeds in direction of replication fork : 1st Okazaki fragme
DNA is the same, almost but not quite. Genetic material: information must contain the information necessary require ~ 460,000 sec (5.3 days) to replicate the entire E. coli chromosome Much strand -Leading strand elongates and 2nd Okazaki fragment made 3rd Okazaki
How do cells decode and use the information in the genome? Cell -> to construct an entire organism. too slow for an organism which divides every 20 min. The enzyme is too abundant ~ connected via DNA ligase.
Nucleus -> Chromosome -> DNA. Replication: capable of precise copying/replication so information is 400 molecules of DNA polymerase I per E. coli cell. Excessive, since generally only 2 Eukaroytic DNA Replication – similarities and differences: Eukaryotes use s
DNA to RNA= transcription, RNA to protein -> translation. not lost of altered. replication forks per cell . The enzyme is not processive enough DNA polymerase I compared to 5 in E.coli. Main polymerases (a, d, e polymerase).
Sequential information= complex mechanism of cipher exists to move Transmission: able to be passed from cell to cell during cell division dissociates after catalysing the incorporation of 20-50 nucleotides . DNA PCNA – proliferating cell nuclear antigen (sliding clamp) .
from a nucleic acid alphabet into an amino acid alphabet. No evidence and parents to offspring. polymerase I cannot initiate DNA synthesis de novo However, shares this particular DNA replication markers used in cancer: MCM activity increased dividing cel
for a reverse. Variation: differences must account for the known variation within problem with every other known DNA polymerase. expression of MCM proteins than normal ones and can also indicate precancer
DNA: phosphate group, 5-C sugar, nitrogen containing base. reach species and among species. DNA polymerase mutants: Confirmed Pol 1 not the replicative polymerase. DNA marker used in breast cancer. PCNA is significantly elevated in proliferating cel
DNA alphabet= A,G (purine, 2) C,T (pyrimidine,3). Griffith 1928: Experiment concluding a chemical substance from one Polymerase I coded for by the PolA1 gene . De luca and Cairns (1969) isolated E.coli prognosis.
Double helix: H bonds, electrostatic repulsion between phosphates and cell is capable of genetically transforming another. mutants that lacked DNA Pol I activity. Cells containing the pola1 mutation are Eukaryotic DNA is replicated from multiple origins: Fragment of replicating D
the base stacking/pairing interactions are often considered to be the 2 Initiation: DNA helicase, single-stranded binding protein (SBB – stops viable (More sensitive to UV light) . Mutation: codon for tryptophan 342 is mutated to replication eyes. Replication fork movement in eukaryotes is ~10 times slower t
major driving forces. One favours helicity (phosphates), other helicity unwound DNA from rejoining), topoisomerase/DNA gyrase(=(reduce a stop codon . PolA1 mutants grow normally – used to search for other DNA form, replication would take 1 month. Chromosomes contain origins every 3-30
(bases). trhe torsional strain caused by the unwinding of the double helix), dnaA. polymerase activities in E.coli (DNA Polymerase II & DNA Polymerase III). Euk helicase loading steps: 1.Origin recognition complex (ORC) bound to ATP
Genetic code is a true code: base can occur in any order, order of bases Primer synthesis: DNA helicase, primase, dnaA. DNA polymerase III:Core enzyme: consists of only those subunits that are required recruits ATP bound Cdc6 3.ORC recruits Mcm2-7 helicase bound to Cdt1 4.Cd
determine the order of amino acids. Elongation: DNA polymerase I & III, SBB, DNA gyrase, DNA ligase. for basic enzymatic activity . Consists of three subunits - Alpha: 5’ to 3’ DNA loading occurs encircling ds DNA 6.Cdc6 and Cdt1 are released 7.ATP is hydro
Redundant: multiple triplets (codons) give rise to same amino acid. DNA replication begins at a origin of replication: starting point. polymerase activity. Epsilon: 3’ to 5’ exonuclease proofreading activity . Theta. loading.
RNA: mRNA, tRNA, rRNA. Bacteria, single origin of replication (a bp sequence of nucleotides DNA polymerase III holoenzyme: DNA Polymerase III holoenzyme – multisubunit Assembly of Eukaryotic replisome: 1. As cells enter S phase of cell cycle two
Nucleic acid: phosphate, 5C sugar, nitrogen containing base. known as oriC). Eukaryotes, multiple origins of replication. DNA strands complex. Consists of 17 polypeptides (make up four subassemblies) 1.Core DDK phosphorylates loaded Mcm2-7 helicase 3. CDK phosphorylates Sld2 and
Difference RNA & DNA: having a hydroxyl group at position 2. U instead unwind at this point. Replication proceeds outwards from 2 replication polymerase: 3 subunits: polymerase (alpha); 3’ to 5’ exonuclease; stimulator of the Together these proteins bind to helicase activating proteins Cdc45 and GINS 6
of T. forks (bidirectional replication). 3’ to 5’ exonuclease 2.Subunit (thetha) responsible for dimerization of the core DNA Cdc45/Mcm2-7/GINS or CMG complex 7. DNA Pol e is recruited for leading stra
DNA double stranded RNA single stranded: base pairing, DNA is used a Initiation & unwinding involves the assembly of a replication fork at an Polymerase 3.Sliding clamp – 2 homodimers (beta), ring structure for processivity released 9. DNA starts unwinding 10. DNA Pol a/primase and d are recruited Fo
template, determined by shape complementarity. origin of replication. Fork is generated by a complex of proteins. Major 4.5 subunits have clamp-loader functions. Sliding clamp (beta ring structures) Euk helicase loading and activation occur during different phases of the c
Transcription: act/process of making copy. One strand of DNA is copied initiator protein is the dnaA protein. Recruits DNA helicase (dnaB - increases Pol III replication efficiency. cycle, helicase loading is permitted but not helicase activation 2.During the res
into a single stranded RNA molecule. One nucleic acid DNA is copied into breaks H bonds) and DNA primase (dnaG) proteins. Helicase bound to DNA polymerases of E.coli : Pol I, II and V function primarily in DNA repair. Pol III- loading is inhibited but loaded helicases are activated.
the form of another RNA. Very little change in ”chemical language”. an inhibitor protein (dnaC) which is released to allow DNA binding at chief DNA-replicating enzyme of E.coli. Eukaryotic DNA replication has additional hurdles: Nucleosome partially di
Structure of DNA not altered. Continued to store information. A gene can replication origin. Helicase begins to break down H bonds & unwind Leading and lagging strands: leading – 3’ to 5’. Lagging 5’ to 3’. replicates past half-nucleosomes. Nucleosomes reassemble from old half-nuc
be copied repeatedly. DNA. An INCORRECT mechanism for DNA replication: Simplest possible way – not histones.
Gene structure: a gene can be defined as discrete region of DNA that is Primer synthesis: primer synthesis marks beginning of synthesis of necessarily correct. Both daughter DNA strands grow continuously incorporating CAF-1 chromosome assembly factor-1. End of chromosomes (Telomeres)
copied (transcribed) into RNA. Gene is transcriptional unit. RNA molecule new DNA molecule. Short stretches of nucleotides (10-12) in length, nucleotides in a complementary fashion (energy provided by 2 terminal DNA replication at telomeres. Solution: Special telomere sequence: tandem
made from the gene is called a transcript. synthesised by an RNA polymerase like complex (Primase; part of a phosphates). Require chain growth in both the 5’ to 3’ direction and the 3’ to 5’ a specific enzyme with integrated RNA template.
DNA sequence: how much of the gene is expressed, when and where -> complex). DNA polymerase can only add deoxyribonucleotide to the 3’- direction. Problem: no enzyme that catalyses 3’ to 5’ nucleotide polymerization How is telomere similar or distinct to DNA polymerase?
promoters. OH group of an existing chain and cannot begin synthesis de novo. After have been found. Dissimilarities: Uses RNA component, No exogenous template required, uses
Transcription is carried out by complex RNA polymerase: RNA elongation is complete, primer removed and replaced with DNA How is 3’ to5’ achieved?: Both daughter DNA strands are polymerized in the 5’ to product. Has helicase activity.
polymerase binds to a specific DNA sequence in front of the gene: the nucleotides. 3’ direction. Leading strand synthesised as one long continuous molecule. Therefore Similarities: requires a template to direct nucleotide addition. Can only extend
promoters. Primosome synthesises RNA primers: 600kdap protein assembly NA synthesized on the lagging strand must be made initially as a series of short DNA nucleotides. Acts in a processive manner. Binds to the DNA substrate.
Promoter: site for RNA polymerase binding. which includes helicase and primase (+5 other subunits). Primase can molecules ( Okazaki fragment ). DNA Repair – DNA replicated with high fidelity: Mis-pairing occurs 1 in 10^8
Terminator: signals the end of transcription. add ribonucleotides de novo. Produces an RNA segment/primer of 11 Okazaki fragments: -Conduct pulse-chase experiments- Involved exposing accuracy arises because: Cells maintain balanced levels of dNTPs reducing ch
Regulatory sequences: site for the binding of regulatory proteins: nucleotides. Works in the 5’ to 3’ direction. replicating DNA to a short ‘pulse’ of radi-labelled nucleotides - Then varying the exhibits a open (inactive) and closed (active) form which helps to properly posit
regulate gene expression. Arthur Kornberg (1957) – E.coli (Dna polymerase I) Added radioactive length of time that the cells would be exposed to a non-labelled nucleotides exonuclease activity of DNA polymerase detects and eliminates the occasiona
Template & Coding strands: only one strand of DNA is copied into RNA. Thymidine triphosphate to DNA polymerase extract from E.coli. When “chase”. Okazaki determined that not all DNA synthesis was a smooth, continuous exist: Action of DNA polymerase I, DNA photolyase, DNA Glycosylase Mismatc
DNA strand is “Read” by RNA polymerase: template strand. DNA strand DNA added (template/source of nucleotides/primer) – DNA process. For the lagging strand, fragments of DNA were synthesised discretely, and Nucleotide excision repair system.
is “not read” during the process = coding strand. RNA transcription will synthesised. assembled later. Sources of DNA damage: Environmental (smoking lots of oxygen, oxides, oxid
have identical sequence to coding strand. Coding strand/sense strand DNA polymerases – enzymes that replicate/synthesise DNA: Pol I- Procedure: Exposed replicating DNA to short pulses ( 5s) of 3H radioactive processed foodpatters of DNA to determine which strand is new and which is p
carried the gene. 928 aa polypeptide (MW-103kDA). Adds the correctly paired nucleotides, followed by addition of excess of normal cold (non-radioactive) Recruits an endonuclease to excise mismatch . Recruits DNA pol III/I to fill in th
Stages of transcription: initiation, elongation & termination. These steps nucleotides to a template strand. Catalysed synthesis of DNA in vitro nucleotides .Resulted in label present only in DNA that synthesized during the short template) . DNA ligase finally reseals the strand. Mutations in MMR genes caus
involve protein-DNA, RNA-ssDNA and RNA-RNA interactions. Proteins when provided with all 4 deoxynucleotide-5;triphosphates, template period of the pulse . DNA then isolated, strands separated in alkaline solution - cancer.
such as RNA polymerase interact with DNA sequences. An RNA-DNA strand and primer. E.coli subsequently found to have several different Various pieces of DNA sorted out by size using sucrose gradient in an MMR: MutS binds to a mismatched base pair. MutL binds to MutS . MutS2MutL
hybrid molecule is produced as the DNA strand is copied into RNA. RNA- DNA polymerases. Incoming dNTP’s form H bonds with template strand ultracentrifuge. Bigger pieces of DNA pptt more rapidly than smaller pieces . Label strand is only partially methylated. MutH endonuclease binds to excises misma
RNA folding is important in transcription termination of some genes. according to AT/GC rule. DNA pol breaks bond between 1st&2nd occurred on two sizes of DNA, one very long, one small of 1000-2000 nucleotides fragment. DNA ligase seals strand.
Translation in prokaryotes and eukaryotes: mRNA leaves nucleus phosphate in dNTP releasing pyrophosphate (Ppi), action provides long. DNA damage by UV: environmental & chemical agents can generate mutation
bound by ribosomes. energy to form a covalent bond between dNMP and nucleotide in Okazaki procedure: Were the smaller fragments artificially induced breakdown dimer formation between 2 adjacent thymine. Distorts DNA and interferes with
Translate the mRNA sequence into protein: protein 20 amino acids. growing chain. products of normally larger pieces? No .Okazaki extended length of exposed pulse Some damage can be directly reversed: DNA photolyases repair pyrimidine
2 nucleotides to one amino acid: 2 nucleotides coding for 1 amino acid Properties of DNA polymerases: whether prokaryotic or euk all share to 30s, a far greater fraction of total label ended up in long DNA strands (similar Chemical mutagens (nitrous acid, dimethyl substrate, acridine orange) : M
would produce 16 possible combination. Not enough to code for 20 the following properties. Incoming base is selected within DNA pol result obtained if period of “cold chase” was prolonged). Therefore fragments 1.Point mutations – in which one base pair replaces another a.Transitions – pur
amino acids. active site by Watson-Crick AT-GC pairing with template strand. Chain existed only temporarily and soon became incorporated into the growing DNA purine (or pyrimidine) b.Transversion – purine replaced by a pyrimidine (or vice
The genetic code: consists of 64 codons, specifies one of 20 AA. growth is in the 5’ to 3’ direction and is anti-parallel to template strand. strands. which one or more nucleotide pairs are inserted or deleted in DNA.
Degenerate: many AA are specified by more than 1 codon. Codons are DNA pol cannot initiate DNA synthesis de novo – require an DNA Polymerase I removes/replaces RNA primer. Because of its 5’ to 3’ Point mutation: change in 1 base of sequence
written 5’ to 3’ as they appear in mRNA. oligonucleotide primer with a free 3’-OH group to build upon. exonuclease activity DNA polymerase I removes RNA primers and fills the gaps . Insertion: base is added
AUG= initiation code, UAA, UAG, UGA are stop codons. Lacks 5’-3’ Pol I has 3 active site: Three distinct activities all within separate parts between Okazaki fragments with DNA Okazaki fragments joined by DNA Ligase. Deletion: base is deleted.
exonuclease activity (editing activity) - There are two forms of the of polypeptide chain; Exhibits 5’ to 3’ polymerase activity (synthesis), 3’ DNA Ligase seals nicks in phosphodiester backbone of DNA where 3’OH is next to a MMR (mismatch repair system): System corrects errors introduced following
enzyme Core enzyme, Holoenzyme to 5’ exonuclease activity (proof reader), 5’ to 3’ exonuclease activity 5’phosphate group. Two classes of DNA ligases :NAD+ as cofactor (E.coli) : ATP as polymerase. Uses methylation er formation (e.g. UV-induced). Light absorbing
Translator molecule= be able to recognise both nucleic acids and AA (editor) . cofactor (T4 DNA Ligase, eukaroytic) - Joins Okazaki fragments together making termed photoreactivation -Photolyase recognises the photodimer and binds to
e.g. tRNA. Klenow fragment of DNA polymerase I: - Pol 1 can be proteolytically lagging strand continuous covalently linked chain - NB. Mutants that were ligase- split the dimer into the original monomers.
How does genetic code work? mRNA contains UGG. ACC of transfer cleaved producing active Klenow fragment (residues 324-928; negative failed to show pulse-chase assembled into larger fragments. Nucleotide excision repair (NER): -All cells have this elaborate pathway to co
RNA carrying a tryptophan aligns to UGG because their shapes are polymerase & 3’ to 5’ exonuclease) Domains separated with trypsin or distortion. In humans NER is the major defence against mutation caused by ca
complementary. subtilisin at amino acid 324. Commonly used DNA polymerase in Base-excision repair involves DNA glycosylases: Certain errors are too subt
RNA is a replicator and capable of metabolism. molecular biology labs (Until Taq polymerase). Used to label DNA recognised by the general repair systems. Free radicals (O2) can damage DNA
Variation: viruses have diverse life cycles. Above the sequence level, fragments for hybridization. oxoguanine). DNA glycosylase cleaves glycosidic bond leaving deoxyribose res
prions can transmit structural information between proteins. Pol I – proof-reader & editor: 3’ exonuclease activity removes site (AP site).
DNA replication: bacterial cell (1-5mil bp). E.coli 4.6mil bp. DNA nucleotides from 3’-end of growing chain- removes incorrect or Repair of AP sites: (due to oxidation of guanine). AP endonucleases recognise
replication: sophisticated, efficient, precise, highly coordinated series of mismatched bases. phosphodiester bond .A stretch of DNA is removed by the enzyme .Resulting ga
molecular events. ligase.
, Initiation of bacterial transcription RNA polymerase is the enzyme that How do we define a gene?: A gene is a unit of DNA, and a protein coding
catalyses the synthesis of RNA .In E. coli, the RNA polymerase holoenzyme Promoter elements are DNA elements where regulatory proteins bind – tra
is composed of : Core enzyme - Five subunit (polypeptides) = a2bb’w. that control the level of gene expression. When a protein coding gene is ‘e
Sigma factor- One subunit (polypeptide) = s . These subunits play distinct polymerase II is the enzyme that transcribes the RNA. The RNA is process
functional roles. (mRNA) – this is ultimately exported to the cytoplasm where it is translate
RNA polymerase holoenzyme: (image below) Eukaryotic gene expression: each gene requires its own promoter and o
Rate of elongation: 50 nucleotides per second. large multi-subunit protein complexes which bind to regulatory DNA sequ
Initiation of bacterial transcription: RNA polymerase holoenzyme binds above basal. Tissue and cell-type specific regulation, gene specific, enviro
Loosely to DNA all along the bacterial chromosome. It scans along the normally organised in operons. Regulatory DNA sequences do not work b
DNA, until it encounters promoter region. When it does transcription regulators. It is the combination of these sequences and ass
The sigma factor recognises both the 35 and 10 regions. It helps to lock the switch to control transcription.
RNA pol to the DNA once a promoter is encountered. Eukaryotic RNA polymerases: Eukaryotes have 3 RNA polymerase enzym
Binding of the RNA pol holoenzyme forms a closed complex. Open RNA. RNA polymerase is the enzyme that synthesises RNA using a DNA te
Transcription is the first step in gene expression: Two fundamental concepts 1. complex formed when TATAAT -10 box is unwound Each RNA pol works in conjunction with its own set of basal transcription
(denatured into two strands) by the holoenzyme. A short RNA strand is complex. Pol II: forms a large complex known as the basal apparatus. Alp
DNA sequence holds biological instruction/ made within the open complex. Sigma factor released. mushroom Amanita phalloides, it inhibits transcription by certain eukaryo
information. Indicate which areas of the DNA are genes and should therefore be End of initiation. Core enzyme now slides down RNA to the gene and begins Gene expression: Constitutive: Some genes are always on at a polymerase II.
expressed. E. coli 4,401 genes encoding 116 RNAs to synthesise an RNA transcript of the gene. Binds constant level, often because the product is required for Basal transcription factors: Transcription factors required by RNA polym
and 4,285 proteins. Human, ~22500 genes (<3% of human genome) Indicate To and reads the template strand. Elongation in bacterial transcription: maintenance of basic cellular function, e.g. Housekeeping genes. all RNA polymerase II promoters.
where transcription should begin and where it open complex 17 bp long. DNA in this region has Regulated: expressed only under certain conditions or in certain Some basics of DNA elements in a promoter region: A typical gene tran
should end. Signals the beginning and end of a gene. 2. Proteins recognise these Been pulled apart into a ”transcription bubble”. On average, the rate of cell/tissue types. Inducible/repressed gene: Responds rapidly to promoter that extends upstream from the site where transcription is initia
RNA synthesis in E.coli is 50 nucleotides per second. specific stimuli (signal etc). After stimulus removed returns to Transcription initiation: RNA Pol II core promoters are DNA sequences a
sequences and carry out the process. Nucleoid Raw ingredients for transcription are ribonucleoside triphosphates basal/inactive state. One stimulus might regulate 1 or more assembly of the transcription machinery and enable transcription initiatio
/cytoplasm in prokaryotes. Nucleus in eukaryotes. (A,U,C,G). genes and could affect one or more cell/tissue types. is the assembly of the pre-initiation complex (PIC). The PIC consists of Po
Transcription: Transcription: act or process of making a copy. One strand of Signal transduction and gene expression: Whether a gene is (GTFs).
the double-stranded gene (DNA) is copied into a single-stranded molecule of expressed depends on signals: internal or external. Figure on PIC assembly is followed by DNA Duplex ‘melting’ and the start of the
RNA. One nucleic acid (DNA) is copied into the form right: A pigment gene is influenced by temperature. Gene C RNA Pol II transcription cycle can be divided into 4 main steps: initiati
of another nucleic acid (RNA). Very little change in ‘chemical language’ . Structure controls fur pigmentation in Himalayan rabbits. Because the promoter region involving assembly of pre-initiation complex (PIC) includi
gene is active when environmental temperatures are between 15 binding protein (TBP) DNA unwound, Pol II synthesised short RNA transcri
of DNA is not altered because of this process. and 25°C, the rabbit reared at 20°C (left) has pigmentation on its clear promoter. Requires phosphorylation of C-terminal (CTD). Pol II trans
Continues to store information. A gene can be copied repeatedly. ears, nose, and feet, where its body loses the most heat. The synthesising longer RNA chains) , elongation (Pol II moves along DNA tem
Gene structure: A gene can be defined as a discrete region of rabbit reared at temperatures above 30°C (right) has no fur regulated by elongation factors enhancing the efficiency and fidelity of tra
DNA that is copied (transcribed) into RNA. A gene is therefore also called a pigmentation, because gene C is inactive at these higher transcriptional pausing and proof-reading), termination (recognition of ter
transcriptional unit. The RNA molecule made from the gene is called a transcript. temperatures. and disengagement of Pol II).
During gene expression, DNA sequences in or near the gene define: How much of What are some ways that signals feed into the control of Transcription initiation is followed by promoter clearance and elonga
transcriptional regulation? – eg cell cycle regulation and growth ‘melt’ DNA to allow polymerase movement. Phosphorylation of the carbo
the gene is expression. When the gene is expression. Where (in cell/ tissue) the
factors, we talked about sugars/metabolic activation in the required for promoter clearance and elongation to begin. Modifications to
gene is expressed. These sequences are termed “promoters” . Transcription is prokaryote/operon lectures. addition, splicing. CTD of Pol II is subject to key phosphorylation events th
carried out by a large protein complex called RNA polymerase . RNA polymerase Termination of bacterial transcription: Termination – end of RNA Gene expression: many levels of regulation: Complex and still clearance and elongation for extra information only and you can do furthe
binds to a specific DNA sequences Infront of the gene – the promoter . The synthesis. Occurs when the short RNA-DNA hybrid of the open complex is incompletely understood. Occurs on many levels: Transcription, more.
promoter attracts RNA polymerase to the gene and “tells” the enzyme that a gene forced to separate. This releases the newly made RNA as well as the RNA post-transcription, translation -Chromatin structure . Regulatory 5’ capping of mRNA: A 5′ cap is formed by adding a G (m7G) to the first e
is nearby. polymerase from the open complex. E.coli has two different mechanisms DNA elements. Basal transcription factors (Pol II/TFIID etc). 5′–5′ link. This takes place during transcription. The cap blocks the 5’ end
Template & coding strand: Only one strand of ds DNA is copied into RNA .DNA for termination. 1. rho-dependent termination -> requires a protein known Regulatory transcription factors and co-factors. RNA: splicing, positions. The cap influences mRNA stability, splicing, export and transla
as r (rho). 2. rho-independent termination (does not require r). stability, processing, regulatory RNAs, modification of RNA, capping process takes place during transcription and may be important fo
strand that is “read” by RNA polymerase = template strand. DNA strand that is localisation. Translation control. The cap structure is recognized by protein factors to influence mRNA stab
P-dependent termination:
“not read” during the process = coding strand .RNA transcript will have identical 3’ ends of mRNA: cleavage of polyadenylation: The sequence AAUAAA
sequence to coding strand (except for the substitution of Thymine by Uracil) of mRNA that is polyadenylated. The reaction requires a protein complex
.Coding strand/Sense strand carries the “gene”. endonuclease, and poly(A) polymerase. The specificity factor and endonu
Stages of transcription: Transcription can be divided into three stages. Initiation. AAUAAA. Poly(A) tail controls mRNA stability and influences translation. T
polymerase add about 200 A residues processively to the 3′ end. The poly
Elongation. Termination . These steps involve protein-DNA, RNA-ssDNA, and
influences translation.
RNA-RNA interactions. Proteins such as RNA polymerase interact with DNA Transcription termination: The mRNA 3′ end formation signals terminat
sequences .An RNA-DNA hybrid molecule is produced as the DNA strand is termination occurs when the polymerase and the nascent RNA are releas
copied into RNA .RNA-RNA folding is important in transcription termination of eukaryotes molecular mechanisms that lead to the timely and efficient di
some genes. remains incompletely understood. Because RNA Pol II transcribes multip
Initiation: The promoter functions as a recognition site for transcription factors. termination occurs in a variety of ways.
The transcription factors enable RNA polymerase to bind to the promoter forming Gene expression: A gene corresponds to a single transcriptional unit – s
terminator. In the case of protein coding genes: Each mRNA consists of an
a closed promoter complex. Following binding, the DNA is denatured into a a coding region, and an untranslated 3′ UTR or trailer.
bubble known as the open promoter complex, or simply an open complex. Many processes regulate gene expression: Transcriptional regulation (c
Elongation: RNA polymerase slides along the DNA in an open complex to (alteration to 5’ and 3’ end and removal of introns). Pre-mRNA (nuclear tra
synthesise the RNA transcript. spliced. Introns removed, exons protein coding sequence).
Termination: a termination signal is reached that causes RNA polymerase to Core promoter: can overlap/include the transcriptional start site (TSS) bi
general basal TF. Shortest sequence at which an RNA polymerase can init
dissociate from the DNA. Proximal promoter: elements act in coordination with the preinitiation co
Transcription in bacteria: Molecular understanding of gene transcription has P-independent termination: r-independent termination is facilitated by 2 sequences in RNA. 1. A uracil-rich sequence located at the 3’ end of the
RNA. 2. A stem-loop structure upstream of the Us. transcription and in regulating frequency of transcription
arisen from bacterial studies. Easier to work with and manipulate than . CCAAT box: 75-80 bases upstream of transcription initiation site, 150 up
eukaryotes. E. coli. Grown quickly, easily, and cheaply in the lab. Gene regulation: regulatory element and transcription factors: How do cells ‘decide’ which genes to express: Different cell types express transcription factors e.g CTF/NF1 family and C/EBP.
Bacterial promoters: Promoters are DNA sequences that “promote” gene different sets of genes. Cells only express roughly 20% of their genes at any one time. Two different cells of the same type may also have different GC box: G-C rich sequence motifs, often found in proximal promoter. Bin
expression. More precisely, they indicate the exact location for the initiation of gene expression patterns depending on their environment and internal state. Gene expression programmes specify the identity and function of transcription.
transcription. Site where RNA polymerase binds to the gene. Promoters are every cell in the human body. Techniques like microarrays (cDNA), RNA-seq (transcriptome), ChIP-seq (identify genes associated with Cis-acting regulatory elements: map ‘near’ to the gene are cis-acting. D
transcription factors) enable large scale determination of gene expression patterns and identify transcription factor specific gene associations. elements
typically located just upstream (5’) of the site where transcription of a gene
actually begins . The bases in a promoter sequence are numbered in relation to
the transcription start site.
