Increase cell density, increase the cell count per unit area, more stiffness -- initiation of EMT.

epithelial-mesenchymal transition

substitution patterns

the hydroxyl groups must be in a syn relationship -- there is restricted rotation around this small ring skeleton.

donation via resonance

highly polarised towards oxygen atom

nucleophilic addition <-> 1,2 addition

treatment of an a b unsaturated ketone with LiAH4 is an addition because the H is added. Likewise, 1,2 addition when gringard adds to ketone. Thiol on 1,4 compound -- addition.

For the hydrohalogenation of the alkenes, we label hydrogen on the double bond. For the addition to carbonyl, we number the oxygen itself.

relates back to alkene addition reactions!

understand and apply the greek nomenclature and relevance to reactivity

really key point, w/k doesn't reduce the nitro to amine, and the clemmenson does

phenol intermediate somewhere there, diaz. salt. phenolic compound esterification chlorinate also going to get the ortho product

conditions for removing t-Butyl Need benzene solvent AlCl3

familiarize with salbutamol synthesis

naphthalene production <br /> remember that FC acylation works for some carboxylic acids

note the mCPBA gives you the ester BUT there is the ester with oxygen bonded, and ester with carbon bonded (minor) ester linkage orientation impacts its directing effect.

use alkyl chains, get di-toluene, nitro then added, then oxidize the alkyl groups to carboxylic acids.

do the alkylation first

then add sulphonyl then the chlorine

nitration NO2 is META bromination reduce the nitro

forming an amide -- acylation of the amine

remember that NaOH and aryl halide yields the phenol

protect amine from protonation

blocking group needed.

1 and 3 the same

FC acylation, reduction (WC reduction)

Rules for free radical substitution Benzylic oxidation -- remember that the powerful oxidant will break C-C bonds. Need benzylic hydrogens to oxidize to the carboxylic acid.

Not the same because ketone to alkyl first reverses polarity so that meta directing substituent becomes o/p directing

1. alkyl group, methyl, not meta directing, o/p instead,
2. polarity reversal
3. carbocation rearrangement

Baeyer-Villiger rxn Electron donating groups on the ring increase rate EWG on ring decrease rate.

A lot of qualities are the opposite in NAS.

Loss of Cl3AlO(-) on carboxylate

Issue of multiple alkylations because the product of alkylation is better nucleophile.

Carbocation rearrangement first, then attack by aromatic ring.

elimination of hydrogen

addition step

Nuclear pore complex or NPC. There is a size exclusion. <60kDa to pass through unassisted.

As soon as this sequence is translated, the SRP binds it. Elongation is temporarily arrested. SRP-ribosome complex binds to the SRP receptor on the ER membrane. Translation now continues into the lumen of the ER. The SPR and its receptor are recycled.

• Axoneme
• Cell crawling via the remodelling of the actin cytoskeleton.

Reuptake or enzymatic breakdown (Ach)

APC/C targets S-CDK and M-CDK. Degradation of M-cylin.

• Provides edge to the cell
• Controls the entry and exit of material.
• Fluid-mosaic model explains the structure and function of the membrane.
• High control of intracellular conditions.

Example of epigenetic change in plants by season.

Crystal violet, CV. In the aqueous solution created, CV exists as its cation CV+. CV+ ions penetrate the cell wall of the bacteria. CV+ binds to negative moieties of the peptidoglycan cell wall. Iodine is added. CV and I- complex and crystallise.

Decolorization, the variable step, strips off the outer membrane of gram negative, but not gram positive bacteria. As the cell wall in gram negative becomes permeable, CVI diffuses out an colour is lost. <br /> Gram positive retains colour from CVI stain.

Safarin is a positively charged counterstain. Binds colourless membrane of gram negative.

Results in pink gram negative and purple gram positive.

Gram staining allows for the differentiation of gram positive and gram negative bacteria.

• Ehrlich's magic bullet.
• Salvarsan brought to market in 1910.
• The systematic selection of compounds, informed by the specific causative agent, still used at present to bring new antibiotics today.

Fleming's serendipitous discovery of penicillin.

• In addition, the Egyptians noted that the yearly river Nile mud gave rise to many frogs so they concluded that this mud spontaneously generated frogs.

Mixing does occur between chromosome regions. Not as distinct as first thought.

Subnuclear structure: nuclear bodies * typically spherical<br /> * PML bodies (promyelocytic leukemia protein), involved in transcriptional regulation/cell division * Cleavage bodies * Cajal bodies (CB) * antibody against coilin * Gems * antibody against SMN * CB and gems co-localise with exposure/differentiation to RA. Vary with cell type. * Nuclei of SMA afflicted foetuses lose gems.

Subnuclear structure: Nuclear speckles, not a blanket term. * Also called interchromatin granule clusters * Splicing factor storage (for splicing factors (mostly) not in use) * Proteins may move out of or enter nuclear speckles.

FRAP as a method to test dynamism, movement. Diffusion vs no diffusion of bleached protein. * Mobile fraction * Immobile fraction

The fibrillar centre is where genes for rRNA are transcribed. The dense fibrillar component where rRNA is processed, chemically modified. The granular component is where protein components are combined with rRNA. Generates preribosomal molecules that are close to being exported to cytoplasm.

Immunoprecipitation is a technique for the isolation of protein or a complex (protein-protein interactions) Sample is combined with a specific antibody for the epitope of interest. The antibody-protein complex is removed and analysed.

1. Molecules from biological sample (lysed) +incubated with antibodies (free or mounted onto support (like agarose bead, magnetic bead))
2. protein A or G coupled beads added.
3. Centrifuged
4. Results in Beads with protein A/G bound to antibody-POI complex.
5. Well separated in this way, differentially based on sedimentation coefficient.

Co-immunoprecipitation (can isolate one type of protein in its complex)

Isolate POI(s) Good with low conc. of POI Protein interactions Unknown proteins Determine if protein is actually being expressed in a given tissue.

Western blot is carried out to analyse the output.

Vary salt and detergent levels to preserve or destroy protein interactions.

mRNA needs to be assisted across the NPC. Like protein, also classed as facilitated diffusion. * mRNP exporter combines with mRNA with poly A tail, by interacting with FG repeats * mRNA moves through NPC * Dpb5 is an RNA helicase * Straightens the mRNA secondary structure and allows passage, removes proteins on the strand (NXT1, NXF1) * mRNP exporter proteins dissociate from the mRNA. * mRNA is now in cytoplasm

An glycerol-ether bond in archaea, an glycerol-ester in bacteria and eukaryotes.

• Margulis hypothesised the popular classical theory for eukaryotic beginnings.
• Later, as an undergraduate, David Baum proposed the inside-out theory. This is where some eoctye, or archaea, lauched protruding blebs at epibiotic protobacteira. This is how the primitive cell would have harnessed another cell's prokaryotic metabolism for its own benefit, evolving into mitochondria, and in doing so, the inversion of cell membrane into two leaflets via engulfment generates the primitive nucleus -- two layers is still seen.

Cells that divide by mitosis

Bacterial chromosomes have a single origin, termed ori, whereas eukaryotic organisms can have many not sequence specific.

Can broadly split the process into three parts. Initiation, elongation and termination

Primase and DNA polymerase A work in close association.

This is the S-phase CDK.

• Replication origin licensing.
• All of this occurs in G1 phase

Orc1-5 complex.

Cdc6 is only present in G1 phase.

DNA replication pathway in humans. Orc complex binds the origin of replication.

Workflow 1. Cross-linking 2. Chromatin fragmentation 3. Immunoprecipitation of chromatin 4. DNA recovery and purification 5. Sequencing of DNA

ChIP-seq is concerned with testing for protein DNA interactions.

NER * Helix distortion * ERCC6 and 8 mutation -- Cockayne's syndrome * XP proteins (XPE or DDB2, XPC, XPA) mutated in xeroderma pigmentosum. * TFIIH, the same helicases as seen in DNA replication.

BER * For non-helix distorting base lesions. * Base is not present, a gap is present in DNA. * Specific DNA glycosylases used for identification. * APEX1 and APEX2 (AP endonucleases): responsible for end processing * An AP site (apurinic/apyrimidinic site). * The exposed 3' OH is available to a replicative polymerase. * Ligation performed by ligase * Short or long patch BER is possible.

MMR. Small insertions and deletion mutation.

In HR, * MRN -- begginings of dsDNA resection. * The PARP1 protein is active on ssDNA. * Free 3' ends made available, crucial for later DNA pol binding. * RPA binds, coats, the ssDNA.<br /> * Rad51 searches for strand for invasion. * Strand invasion carried out by sister chromatid, etc. * D-loop formation.

May have. * DSBR * SDSA * BIR

NHEJ relies on microhomologies. Doesn't require homologous sequence from another source. * Ku protein instrumental in identification of DSB and recruits DNA-PKcs. * DNa-PKcs autophosphorylates. * DNA ends processed by Artemis. * LIG4 and XCRR4 are needed for strand ligation.

NHEJ and HR can be compared.

TEs are transposable elements.

Transposons are mobile DNA elements.Can move throughout the genome. Can be catagorised as class 1 (retrotransposons) or class 2 (DNA transposons).

Class 1 comprises TEs with LTRs, retroposons (LINE), SINEs.

Class 2 comprises TEs that operate under replicative transposition or non-replicative transposition. Replicative transposition (nick and paste) -- a total of two TEs as an end result, one as part of the donor and one as part of the target sequence. cointegrate.

Non-replicative transposition (cut and paste) - only one TE generated, in the target.

Examples of DNA-only transposon:

The initial sample consisted of 1 band. F = 0. 1st generation = The sample overall less dense, still one band. Intermediate density. dsDNA made of one strand heavy and one light. After 2 generations, there was a band for intermediate density and for strands of just light, N-14, dsDNA.

Three methods of replication were initially hypothesized: * Conservative * Semi-conservative * Dispersive

Semi-conservative method was eventually determined to be correct based on empirical evidence from Messelson & Stahl, in 1958.

Parental strands consist of N-15 isotopes. Replicated daughter strands consist of N-14 isotopes. The CsCl ultracentrifugation process creates density gradient. This allows DNA fragments of different densities to migrate and form a band at the point at which their buoyant density equals that of the salt.

1. E.coli grown in an heavy nitrogen, N-15, enriched medium
2. Then transferred to N-14 based media to reproduce
3. As several points in the experiment, cells were lysed and underwent ultracentrifugation through a CsCl concentration gradient

• Denature
• Annealing primer
• Synthesize new DNA with polymerase

• High speed
• Extreme sensitivity

Antioxidant Ebselen + COPD

COPD characterised by

lncRNAs

3'-5' phosphodiester linkage

Carbohydrate terminology

Synthetic route

• Purines have a 2-ring heterocycle.
• Pyrimidines only have one.

When there is a nucleobase present, the anomeric position on the sugar is labeled 1'

Nucleosides have a nitrogenous base and a five-carbon carbohydrate group, usually a ribose molecule. Nucleotides are a nucleoside with one or more phosphate groups attached.

Hemiacetals

Middle down MS technique

Branched chains contain at least one ubiquitin subunit that is simultaneously modified on multiple acceptor sites, Michael E. French, Chad F. Koehler & Tony Hunter, 2021

NF-kappaB, "nuclear factor kappa-light-chain-enhancer of activated B cells"

indicated in pathologies such as * cancer * immune defects * neurodegeneration