1) The document discusses the conformations of fused ring cycloalkanes, using decalin as an example. It describes the chair and boat conformations of cyclohexane and why the chair form is more stable.
2) It also discusses the rapid inversion of the cyclohexane ring and the preference for substituents to be in the equatorial position. This provides insight into the stereochemistry of fused ring compounds.
3) Understanding conformations is important for organic synthesis as it provides information about the spatial arrangements of atoms and how they change during chemical reactions.
The video lecture for this presentation is available at the following link on YouTube
https://youtu.be/3sxal579RNM
The presenation will be useful for Ug/PG (Chemistry) students
An organic species which has a carbon atom bearing only six electrons in its outermost shell and has a positive charge is called carbocation.
The positively charged carbon of carbocation is sp2 hybridized.
The unhybridized p-orbital remains vacant.
They are highly reactive and act as reaction intermediate.
They are also called carbonium ion.
The video lecture for this presentation is available at the following link on YouTube
https://youtu.be/3sxal579RNM
The presenation will be useful for Ug/PG (Chemistry) students
An organic species which has a carbon atom bearing only six electrons in its outermost shell and has a positive charge is called carbocation.
The positively charged carbon of carbocation is sp2 hybridized.
The unhybridized p-orbital remains vacant.
They are highly reactive and act as reaction intermediate.
They are also called carbonium ion.
Two dimensional Nuclear Magnetic Resonance (2D NMR) refers to a set of multi pulse techniques which were introduced to overcome the complex spectra obtained with NMR.
It is a set of NMR methods which give data plotted in a space defined by two frequency axes rather than one.
more chemistry contents are available
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Organic Synthesis:
The Disconnection Approach
One Group C-C Disconnection of Alcohol and Alkene
Two dimensional Nuclear Magnetic Resonance (2D NMR) refers to a set of multi pulse techniques which were introduced to overcome the complex spectra obtained with NMR.
It is a set of NMR methods which give data plotted in a space defined by two frequency axes rather than one.
more chemistry contents are available
1. pdf file on Termmate: https://www.termmate.com/rabia.aziz
2. YouTube: https://www.youtube.com/channel/UCKxWnNdskGHnZFS0h1QRTEA
3. Facebook: https://web.facebook.com/Chemist.Rabia.Aziz/
4. Blogger: https://chemistry-academy.blogspot.com/
Organic Synthesis:
The Disconnection Approach
One Group C-C Disconnection of Alcohol and Alkene
Conformational isomerism
Conformations of Ethane:
Conformations of Cyclohexane
Representation of conformations:
Sawhorse projection:
Newman projection:
The conformational analysis of cyclohexane
CONFORMATION OF MONO SUBSTITUTED CYCLOHEXANE
Stereo chemistry of substitute cyclohexane presentationMUKULsethi5
this video very useful for all chemistry related exam like
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in this we discuss stereochemistry of substitute cyclohexane.
we discuss about
1,3 diaxal interaction
1,2 interaction
mono substitute cyclohexane
Conformation of Cyclohexane
Stereochemical configuration of cyclohexane
Newman projection of cyclohexane
Repulsion energy of substituent in cyclohexane
Conformational analysis of medium ringsPRUTHVIRAJ K
Conformational analysis of medium rings: Spatial arrangement and conformation of 7membered, 8membered, 9 and 10membered rings, nature of hydrogen and carbon atoms
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
2. INTRODUCTION
• Molecules with multiple rings are very common in nature.A
prime example is the steroid structure, exemplified by the
common oral contraceptive ethinyl estradiol.
• Here, we are discussing two cyclohexane
rings are bonded to each other in
most common way- with the two
ring junctions (“bridgeheads”)on
adjacent carbons, a situation called fused rings. The parent
molecule is called decalin since there are ten carbon in total.
8. Many Bicyclic Systems
• There are many important structures that result when one
ring is fused to another.
• Camphor, which you smelled the first day of class, and
camphene are fragrant natural products isolated from
evergreens.
9. Bicyclic Compounds
Nomenclature
The two molecules are not identical, therefore they cannot have
the same name.
Count the number of carbons connecting the
bridgeheads.
10. Bicyclic Compounds
Nomenclature
• Representing compounds with two fused rings.
• To name a bicyclic compound, include the prefix “bicyclo” in front of the total
carbon alkane name. For example, the compounds below could both be named,
bicycloheptane.
11. Conformation:
• Conformation cycloalkane fused ring is same as
that of cyclohexane. Let us consider cyclohaxane. If
the carbons of a cyclohexane ring were placed at
the corners of a regular planar hexagon, all the C-
C-C bond angles would have to be 120". Because
the expected normal C-C-C bond angle should be
near the tetrahedral value of 109.5", the suggested
planar configuration of cyclohexane would have
angle strain at each of the carbons, and would
correspond to less stable cyclohexane molecules
than those with more normal bond angles. The
actual normal value for the C-C-C bond angle of an
open-chain -CH2-CH,-CH2- unit appears to be
about 112.5", which is 3 times greater than the
tetrahedral value. From this we can conclude that
the angle strain at each carbon of a planar
cyclohexane would be (120" - 112.5") = 7.5". Angle
strain is not the whole story with regard to the
instability of the planar form, because in addition
to having C-C-C bond angles different from their
normal values, the planar structure also has its
carbons and hydrogens in the unfavorable eclipsed
arrangement.
Cyclohexane in the
strained planar
configuration showing
how the hydrogens
become eclipsed during
fused ring formation
12. Examples: Chair and Boat
form configurations.
• If the carbon valence angles are kept near the tetrahedral value,
you will find that you can construct ball-and-stick models of the
cyclohexane six-carbon ring with two quite different
conformations.
• These are known as the "chair" and "boat" conformations .
• It has not been possible to separate cyclohexane at room
temperature into pure isomeric forms that correspond to these
conformations, and actually the two forms appear to be rapidly
interconverted. The chair conformation is considerably more
stable and comprises more than 99.9% of the equilibrium mixture
at room temperature.
Chair (left) and boat (right) conformations of the six carbons of a cyclohexane ring
with normal C-C-C bond angles.
13. Doyouknow?
Whyistheboatformlessstablethanthechairform,if
bothhavenormalC-C-Cbondangles?
• The answer is that the boat form has unfavorable non-
bonded interactions between the hydrogen atoms around
the ring. If we make all of the bond angles normal and
orient the carbons to give the "extreme boat"
conformation ,a pair of 1,4 hydrogens (the so-called
"flagpole" hydrogens) have to be very close together (1.83
A). Hydrogens this close together would be on the rising
part of a repulsion potential energy curve, for hydrogen-
hydrogen non-bonded interactions. This steric hindrance
at an H-H distance of 1.83 A corresponds to a repulsion
energy of about 3 kcal mole-l. There is still another factor
that makes the extreme boat form unfavorable; namely,
that the eight hydrogens along the "sides" of the boat are
eclipsed, which brings them substantially closer together
than they would be in a staggered arrangement (about
2.27 A compared with 2.50 A). This is in striking contrast
with the chair form.
14. Do you know?
Differencebetweenchairand boat
conformation
• The chair structure is quite rigid, and rotation does
not occur around the C-C bonds with interconversion
to the boat structure. In contrast, the boat form is
quite flexible. Rotation about the C-C bonds permits
the ring to twist one way or the other from the extreme
boat conformation to considerably more stable, equal-
energy conformations, in which the flagpole hydrogens
move farther apart and the eight hydrogens along the
sides become largely but not completely staggered.
These arrangements are called the twist-boat
(sometimes skew-boat) con- formations and are
believed to be about 5 kcal mole-l less stable than the
chair form.
16. ConformationalEquilibriaand Equilibration
for Cyclohexanefusedrings
• Case 2:There are two distinct kinds of hydrogen in the
chair form of cyclohexane- six that are close to the
"average" plane of the ring (called equatorial hydrogens)
and three above and three below this average plane
(called axial hydrogens). This raises interesting questions
in connection with substituted cyclohexane. For example,
is the methyl group in methyl- cyclohexane equatorial or
axial. Since only one methyl cyclohexane is known, the
methyl group must be exclusively equatorial, exclusively
axial, or the two forms must be interconverted so rapidly
that they cannot be separated into isomeric forms. It
appears that the latter circumstance prevails, with the
ring changing rapidly from one chair form to another by
flipping one end of the chair up and the other end down.
This process is called ring inversion and it is process is
called ring frequency.
17. • Case 3: With cyclohexane, inversion is so fast at room
temperature t, on the average, the molecules flip about
100,000 times per second, over an energy barrier of
about 11 kcal mole-l. You will understand this flipping
process if you make a model of a cyclohexane ring
carrying a single substituent. By manipulating the
model you can discover some of the different ways the
process can occur. The simplest route is simply to flip
up one corner of the ring to convert the chair into a
boat and then flip down the opposite carbon:
• Because of the flexibility of the boat conformation, it is
possible to transform it to other boat conformations whereby
carbons other than the one indicated flip down and complete
the interconversion. At
Because of the flexibility of the boat conformation, it is possible to
transform it to other boat conformations whereby carbons other than
the one indicated flip down and complete the interconversion.
18. • Case 4: At room temperature the conformation of methyl
cyclohexane with the methyl equatorial is more stable than
the one with the methyl axial by 1.7 kcal molep1. The same is
true of all mono substituted cyclohexanes to a greater or
lesser degree. Reasons for this can be seen from space-filling
models (Figure 12-8), which show that a substituent group
has more room when the substituent is equatorial than when
it is axial. In the axial position the substituent is
considerably closer to the two axial hydrogens on the same
side of the ring than to other hydrogens, even hydrogens on
adjacent carbons when the substituent is in the equatorial
position.
equatorial
axial
Space-filling models of equatorial and axial chair conformations of
cyclohexyl bromide. Significant non bonded interactions are indicated for
the sawhorse formulas by dashed lines; these inter- actions are more severe
in the axial than the equatorial conformation.
19. Importanceof conformationof fusedrings in
organic synthesis:
• It`s gives information about stereochemistry of cyclohaxane
and their derivatives.
• It`s tells about difference spatial rearrangement of atoms
during passage of chemical reaction.
• It`s is useful in organic synthesis of macromolecules.
20. Reference:1. Seventh edition, Organic Chemistry by Robert Thornton Morrison, Robert Neilson Boyd, Saibal
Kanti Bhattacharjee.
2. Cycloalkanes, Cycloalkanes, and Cycloalkanes, Cyclohexane Conformations , Conformational
Equilibria and Equilibration for Cyclohexane Derivatives.
3. Google, Scifinder.
4. Journals of American chemical society.
5. Journals of Royal chemical society.
6. International Journal of Organic Chemistry.
7. https://www.researchgate.net/publication.
8. Major reference material Hill & Kolb, CHEMISTRY FOR CHANGING TIMES, 9th Ed, pp566-
573.
9. Grant, Ellen Dr. “ THE BITTER PILL” 1985 & “SEXUAL CHEMISTRY”1996.
10. Marschall, L., “The Sciences” p.1111, Nov/Dec1995. (This reference has the quote from Sanger
concerning reason for “pill” development).