This document provides an overview of protein structure and function. It discusses the four levels of protein structure: primary, secondary, tertiary, and quaternary structure. The primary structure is the amino acid sequence. Secondary structures include alpha helices and beta sheets formed by hydrogen bonding. Tertiary structure describes the overall 3D shape formed by interactions between amino acid side chains. Quaternary structure involves the clustering of multiple peptide chains. Finally, it outlines several key functions of proteins, including structural proteins, transport proteins, and enzymes/receptors.
Amino acisd structure
Peptide bond formation
Analysis of protein Structure- X-ray Crystallography
Different structural levels of proteins with examples.
Importance of protein structure
Creutzfeldt-Jacob-Disease due to changes in normal protein conformation.
Amino acisd structure
Peptide bond formation
Analysis of protein Structure- X-ray Crystallography
Different structural levels of proteins with examples.
Importance of protein structure
Creutzfeldt-Jacob-Disease due to changes in normal protein conformation.
A protein needs to adopt a final and stable 3-dimensional shape in order to function properly.
• The Tertiary Structure of a protein is the arrangement of the secondary structures into this
final 3-dimensional shape.
the topic introduction of protein cover their target their primary structure , secondary structure and tertiary structure and their bonding interaction
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.
A protein needs to adopt a final and stable 3-dimensional shape in order to function properly.
• The Tertiary Structure of a protein is the arrangement of the secondary structures into this
final 3-dimensional shape.
the topic introduction of protein cover their target their primary structure , secondary structure and tertiary structure and their bonding interaction
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.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
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 .
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
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.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
Richard's aventures in two entangled wonderlandsRichard 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.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
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.
2. CONTENT
• INTRODUCTION
• AMINO ACID
• PEPTIDE BOND FORMATION
• PROTEIN
• STRUCTURE OF PROTEIN
PRIMARY STRUCTURE
SECONDARY STRUCTURE
TERTIARY STRUCTURE
QUATERNARY STRUCTURE
FUNCTION OF PROTEIN
STRUCTURAL PROTEINS
TRANSPORT PROTEINS
ENZYME AND RECEPTORS
3. INTRODUCTION
• Proteins are the most abundant organic molecules of the living
system.
• They constitute about 50% of the cellular dry weight.
• A They constitute the fundamental basis of structure and
function of life.
• In 1839, Dutch chemist GJ. Mulder was first to describe about
proteins.
• The term protein is derived from a Greek word proteios,
meaning first place.
• The proteins are nitrogenous macromolecules that are
composed of many amino acids.
4. AMINO ACID
• Amino acids are a group of organic compounds containing two
functional groups – amino and carboxyl.
• The amino group [ -NH₂] is basic while the carboxyl group [- COOH] is
acidic in nature.
• There are about 300 amino acids occur in nature. Only 20 of them occur
in proteins.
5.
6. PEPTIDE BOND FORMATION
• a-carboxyl group of one amino acid (with side
chain R1) forms a covalent peptide bond with a-
amino group of another amino acid (with side
chain R2) by removal of a molecule of water.
• The result is. Dipeptide.
• The dipeptide can then form a second peptide
bond with a third amino acid( with side chain R3)
to give tripeptide.
• petition of this process generates a polypeptide or
protein of specific aminoacid sequence.
• Has 40% double bond character, caused by
resonance.
7. PROTEIN
• Proteins are polypeptide structures consisting of one or more
long chains of amino acid residues.
• They carry out a wide variety of organism functions, including
DNA replication, transporting molecules, catalyzing metabolic
reactions, and providing structural support to cells.
8. STRUCTURE OF PROTEINS
• Proteins have different levels of organization
• Primary Structure
• Secondary Structure
• Tertiary Structure
• Quaternary Structure
9. PRIMARY STRUCTURE
• The primary structure of protein refers to the sequence of
amino acids present in the polypeptide chain.
• Amino acids are covalently linked by peptide bonds or covalent
bonds.
• Each component amino acid in a polypeptide is called a
"residue" or moiety.
• By convention the primary structure of protein starts from the
amino terminal (N) end and ends in the carboxyl terminal (C)
end.
10. SECONDARY STRUCTURE
• It is a local, regularly occurring structure in proteins and is
mainly formed through hydrogen bonds between backbone
atoms.
• Pauling & Corey studied the secondary structures and proposed
2 conformations.
α-helix.
ẞ sheets.
11. α-helix
• Right handed spiral structure.
• Side chain extend outwards.
• Stabilized by H bonding that are arranged such that the
peptide Carbonyl oxygen (nth residue) and amide
hydrogen(n+4 th residue).
• Amino acids per turn - 3.6
• Pitch is 5.4 A°
• Alpha helical segments, are found in many globular proteins
like myoglobin, troponin C.
• Length 12 residues and -3 helical turns.
• phi-60 degrees, psi = -45 degrees. falls within the fully
allowed regions of the Ramachandran diagram.
12. ẞ PLEATED SHEETS
• Formed when 2 or more polypeptides line up side by side.
• Individual polypeptide- beta strand.
• Each beta strand is fully extended.
• They are stabilized by hydrogen bond between N- H and
carbonyl groups of adjacent chains.
13. Beta sheets come in two varieties
• Antiparallel beta sheet - neighboring hydrogen bonded
polypeptide chains run in opposite direction.
• Parallel beta Sheet - hydrogen bonded chains extend in the
same direction.
• The connection between two antiparallel strands may be just a
small loop but the link between tandem parallel strands must
be a crossover connection that is out of the plane of the ẞ
sheet.
14. TERTIARY STRUCTURE
• The tertiary structure defines the specific overall 3-D shape of the
protein.
• Tertiary structure is based on various types of interactions between
the side-chains of the peptide chain.
Interactions stabilizing tertiary structure :
• 1. Disulfide bonds
• 2. Hydrophobic interactions
• 3. Hydrogen bonds
• 4. Ionic interactions
• 5. Vander Waals force
15. . DISULFIDE BONDS
• Covalent bond between sulfur atoms on two cysteine amino
acids.
16. HYDROPHOBIC INTERACTIONS
• Close attraction of non-polar R groups through dispersion
forces.
• They are non attractive interactions, but results from the
inability of water to form hydrogen bonds with certain side
chains.
• Very weak but collective interactions over large area stabilize
structure.
• Repel polar and charged molecules/particles.
17. HYDROGEN BONDS
• H bonds are weak which allows to be broken and reformed
easily.
• Allows structural change and produces ‘functional molecules’
18. IONIC INTERACTIONS
• lons on R groups form salt bridges through ionic bonds.
• NH3+ and COO- areas of the protein attract and form ionic
bonds.
19. VANDER WAALS FORCE
Van der Waals (dispersion) forces contribute to interactions of proteins
with other molecules or with surfaces, but because of the structural
complexity of protein molecules, the magnitude of these effects is usually
estimated based on idealized models of the molecular geometry, e.g.,
spheres or spheroids.
20. • The quaternary protein structure involves the clustering of several individual
peptide or protein chains into a final specific shape.
• A variety of bonding interactions including hydrogen bonding, salt bridges,
and disulfide bonds hold the nvarious chains into a particular geometry.
• Two kinds of quaternary structures, both are multi-subunit proteins.
Homodimer- association between identical polypeptide chains.
Heterodimer -interactions between subunits of very different structures.
• The interactions within multi subunits are the same as that found in tertiary
and secondary structures
QUATERNARY STRUCTURE
22. STRUCTURAL PROTEINS
• For example, structural proteins maintain cell shape, akin to a
skeleton, and they compose structural elements in connective
tissues like cartilage and bone in vertebrates. Enzymes are
another type of protein, and these molecules catalyze the
biochemical reactions that occur in cells.
23. TRANSPORT PROTEINS
• Transport proteins, also known as transmembrane proteins, are
membrane proteins that aid in the facilitated diffusion or active
transport of ions across the hydrophobic lipid bilayer. Such
proteins include channel proteins, carrier proteins, sodium-
potassium pumps, GLUT1, proton pump, calcium ATPase, and
others.
24. ENZYME AND RECEPTORS
Enzyme linked receptors or catalytic receptors are a group of
multisubunit transmembrane protein and the second major type
of cell surface receptor. They promote several processes in
animal cells such as cell proliferation, differentiation, cell growth,
cell survival once recognized by specific ligands.
