Lipids Chemistry Structure & Function (More Detailed)hafizayyub
This presentation is for Medical students. It is more detailed explanation of Lipids including types and medical importance. It is made by Drs Charles Stephen and Dr Ayyub Patel
This Presentation Deals With The Proteins And Their Different Structures. In This Presentation, You Will Learn About What Are Proteins, Importance Of Proteins, Structures Of Proteins, Primary Structure, Secondary Structure, Tertiery Structure, Quaternery Structure, Biological Examples With References For Further Studies.
Describes the structural organisation of proteins with example and its determination, interrelationship b/w structure and function of proteins, also biologically important peptides is covered.
by Dr. N. Sivaranjani, MD
Tertiary Structure basically of Hydrophobic interactions, (interactions in side chains), hydrogen bonding, salt bridges, Vander Waals interactions.
e.g. Globular proteins & Fibrous Proteins
Gives in detail primary, secondary, tertiary and Quaternary structure of proteins. Gives classification of secondary structure: alpha helix, beta pleated sheet and different types of tight turns and explains most commonly found tight turn in proteins i.e. beta turn. Briefs about the Ramachandran plot of proteins, dihedral or torsion angles and explains why glycine and proline act as alpha helix breakers. Explains tertiary structure of proteins and different covalent and non covalent bonds in the tertiary structure and relative importance of these bonding interactions. Details about the quaternary structure of proteins and explains why hemoglobin is a quaternary protein and insulin is not.
Lipids Chemistry Structure & Function (More Detailed)hafizayyub
This presentation is for Medical students. It is more detailed explanation of Lipids including types and medical importance. It is made by Drs Charles Stephen and Dr Ayyub Patel
This Presentation Deals With The Proteins And Their Different Structures. In This Presentation, You Will Learn About What Are Proteins, Importance Of Proteins, Structures Of Proteins, Primary Structure, Secondary Structure, Tertiery Structure, Quaternery Structure, Biological Examples With References For Further Studies.
Describes the structural organisation of proteins with example and its determination, interrelationship b/w structure and function of proteins, also biologically important peptides is covered.
by Dr. N. Sivaranjani, MD
Tertiary Structure basically of Hydrophobic interactions, (interactions in side chains), hydrogen bonding, salt bridges, Vander Waals interactions.
e.g. Globular proteins & Fibrous Proteins
Gives in detail primary, secondary, tertiary and Quaternary structure of proteins. Gives classification of secondary structure: alpha helix, beta pleated sheet and different types of tight turns and explains most commonly found tight turn in proteins i.e. beta turn. Briefs about the Ramachandran plot of proteins, dihedral or torsion angles and explains why glycine and proline act as alpha helix breakers. Explains tertiary structure of proteins and different covalent and non covalent bonds in the tertiary structure and relative importance of these bonding interactions. Details about the quaternary structure of proteins and explains why hemoglobin is a quaternary protein and insulin is not.
protein chemistry, Biochemistry
the different level of organisation of the protein .
detail on individual structure and the bonds stabilising the structure of the protein.
Structure of protiens and the applied aspectsMohit Adhikary
The slides explain the structures of proteins, the bond stabilizing the structure of amino acids, the different types of protein structures, the applied aspects and the newer advances in the protein structure.
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 .
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.
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.
This pdf is about the Schizophrenia.
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1. HBC1011 Biochemistry I
Trimester I, 2018/2019
Lecture 7 – Protein structure and
function
Ng Chong Han, PhD
MNAR1010, 06-2523751
chng@mmu.edu.my
1
2. Overview
• Conformation of the peptide group
• Secondary structures
– Alpha helix
– Beta sheet
– Turns and loops
2
3. The conformation of the peptide group
• The structure of peptides are flexible and yet
conformationally restricted
• Geometry of protein backbone:
– peptide bond is essentially planar
– 6 atoms lie in the same plane
• Nature of the chemical bonding:
– peptide bond has considerable double-bond character, it
is restricted to one of two possible conformations, either
trans or cis.
– constrains the conformation of the peptide backbone and
accounts for the bond's planarity.
3
4. Peptide Bonds Are Planar. In a pair of linked amino acids, six atoms (Cα, C, O, N, H,
and Cα) lie in a plane. Side chains are shown as green balls.
1
2
3
4
5
6
4
5. Cis and trans conformations
• Two conformations are possible for a planar peptide bond.
• Trans conformation: 2 α-carbon atoms are on opposite
sides of the peptide bond.
• Cis conformation: these groups are on the same side of the
peptide bond.
• Almost all peptide bonds in proteins are trans because cis
conformation create more steric hindrance between the
side chains attached to the two α-carbon atoms, making
them energetically unfavorable.
5
6. Cis and trans conformations
6
The trans form is strongly favored because of steric clashes
that occur in the cis form.
Green: side chain
7. Dihedral angles
• Two dihedral angles in
the peptide bond
determine the local
shape assumed by the
protein backbone.
• Bonds between the
amino group and the
α-carbon atom and
between the α-carbon
atom and the carbonyl
group are pure single
bonds.
7
8. Dihedral angles
• The two adjacent rigid
peptide units may
rotate about these
bonds, taking on
various orientations.
• This freedom of
rotation about two
bonds of each amino
acid allows proteins to
fold in many different
ways.
8
9. Dihedral angles
9
• The rotations about these bonds can be specified by dihedral angles.
• The angle of rotation about the bond between the nitrogen and the
𝛂-atoms is called phi (𝛟).
• The angle of rotation about the bond between the 𝛂-carbon and the
carbonyl carbon atoms is called psi (𝛙).
• A clockwise rotation about either bond as viewed from the front of
the back group corresponds to a positive value.
• The 𝛟 and 𝛙 angles determine the path of the polypeptide chain.
10. Ramachandran diagram
10
Are all combination of 𝛟 and 𝛙 possible?
G. N. Ramachandran recognized that many combinations are
forbidden because of steric collisions between atoms. The values
can be visualized on a 2D plot called Ramachandran diagram.
Three-quarters of the possible (𝛟 and 𝛙) combinations are
excluded simply by local steric clashes.
The most favorable regions are
shown in dark green; borderline
regions are shown in light
green. The structure on the
right is disfavored because of
steric clashes.
12. Secondary structure
• Protein secondary structure can be described by the hydrogen-
bonding pattern of the peptide backbone of the protein.
• The most common 2nd structures: alpha (α) helices and beta (β)
sheets/beta strands
• Other 2nd structures: β turn, omega (Ω) loop
• Alpha helices, beta strands and turns are formed by a regular
pattern of hydrogen bonds between the peptide N-H and C=O
groups of amino acids that near each one another in the linear
sequence.
12
13. • Linus Carl Pauling (February 28, 1901 –
August 19, 1994): American quantum chemist
and biochemist.
• Two Nobel prizes winner
• Awarded the Nobel Prize in chemistry for his
work describing the nature of chemical bonds.
The elucidation of the structure
of the α-helix is a landmark in
biochemistry because it
demonstrated that the
conformation of a polypeptide
chain can be predicted if the
properties of its components
are rigorously and precisely
known. 13
14. Alpha-helix
• A coiled rod-like
backbone structure forms
the inner part of the rod
and the side chains
extend outward in a
helical array.
• The α-helix is stabilized
by intrachain hydrogen
bonds (intra-strand)
between the NH and CO
groups of the main chain.
14
16. Alpha-helix
• Each residue is related to the next one by
a rise of 1.5 Å (angstrom, 1Å = 0.1nm)
along the helix axis and a rotation of 100º,
which gives 3.6 amino acid residues per
turn of helix.
• Amino acids spaced three and four apart
in the sequence are spatially quite close to
one another in an α-helix.
16
17. Alpha-helix
• The Ramachandran diagram (for
visualization of dihedral angles)
reveals that both right-handed
and the left handed helices are
possible conformations.
• However, essentially all α helices
in proteins are right-handed.
• Right-handed helices are
energetically more favorable
because there is less steric clash
between the side chains and the
backbone.
17
18. Schematic Views of α-Helices. (A) A ball-and-stick model. (B) A ribbon
depiction. (C) A cylindrical depiction. 18
19. A Largely α-Helical Protein. Ferritin, an iron-storage protein,
is built from a bundle of α helices.
19
20. Beta structure : beta strand
• β structure : β strands and β sheets
• A polypeptide chain, called a β strand is almost fully
extended rather than being tightly coiled as in the α helix.
• Beta sheet are stabilized by hydrogen bonding between
polypeptide strands (inter-strand).
• The distance between adjacent amino acids along a β
strand is approximately 3.5 Å
• The side chains of adjacent amino acids point in opposite
directions.
• β strands are rare because they are conformationally less
stable. However, when two adjacent β strands line up they
can form hydrogen bonds. This creates a β sheet.
20
21. Structure of a β-Strand. The side chains are alternately
above and below the plane of the strand.
7 Å
21
22. Beta sheet - Antiparallel
• When multiple β strands are arranged side-by-side, they
form β sheets.
• Adjacent chains in a β sheet can run in opposite
directions (antiparallel β sheet) or in the same direction
(parallel β sheet).
• Antiparallel arrangement: NH group & CO group of each
amino acid are respectively hydrogen bonded to the CO
group and the NH group of a partner on the adjacent
chain
22
23. An Antiparallel β Sheet. Adjacent β strands run in opposite directions.
Hydrogen bonds between NH and CO groups connect each amino acid to a
single amino acid on an adjacent strand, stabilizing the structure. The
hydrogen bonds are essentially perpendicular to the β strands, and the
space in between is alternately wide and narrow.
23
24. Beta sheet - Parallel
• Parallel arrangement: for each amino acid, the NH group is
hydrogen bonded to the CO group of one amino acid on
the adjacent strand, whereas the CO group is H-bonded to
the NH group on the amino acid two residues farther along
the chain.
• Parallel sheets are less stable than antiparallel sheet,
possibly because the hydrogen bonds are distorted.
• Many strands, typically 4 or 5 but as many as 10 or more,
can come together in β sheets. Such β sheets can be
purely antiparallel, purely parallel, or mixed.
24
25. A Parallel β Sheet. Adjacent β strands run in the same direction.
Hydrogen bonds connect each amino acid on one strand with two
different amino acids on the adjacent strand. The hydrogen bonds are
evenly spaced but slanted.
25
27. Beta sheet
• In schematic diagrams: depicted by broad arrows pointing
in the direction of the carboxyl-terminal end to indicate the
type of β sheet.
• can be relatively flat but most adopt a somewhat twisted
shape.
• important structural element in many proteins. i.e.: fatty
acid-binding proteins, important for lipid metabolism, are
built almost entirely from β sheets
27
28. A Twisted β Sheet. (A) A ball-and-stick model. (B) A schematic model. (C)
The schematic view rotated by 90 degrees to illustrate the twist more
clearly. 28
29. A Protein Rich in β Sheets.
The structure of a fatty acid-
binding protein.
29
30. Polypeptide chains can change
direction by making reverse turns & loops
• Most proteins required reversals in the direction of their
polypeptide chains.
• Reversals: reverse turn (also known as the β turn or hairpin
bend)
• Reverse turns: CO group of residue i of a polypeptide is H-
bonded to the NH group of residue i + 3.
• This interaction stabilizes abrupt changes in direction of the
polypeptide chain.
30
31. Structure of a
Reverse Turn.
The CO group of
residue i of the
polypeptide chain is
hydrogen bonded to
the NH group of
residue i + 3 to
stabilize the turn.
H bond stabilizes
the bend.
31
32. Loops
• Unlike α helices and β strands, loops do not have regular,
periodic structures.
• Nonetheless, loop structures are often rigid and well
defined.
• Turns and loops invariably lie on the surfaces of proteins:
often participate in interactions between proteins & other
molecules.
• secondary structure: α helices, β strands, and turns along a
protein chain.
32
33. Loops on a Protein Surface.
A part of an antibody molecule
has surface loops that mediate
interactions with other
molecules.
33
34. Amino acid have different propensities for
forming α helices, β sheets and turns
• Amino acids vary in their ability to form 2nd structure
elements.
• Proline and glycine are sometimes known as "helix
breakers" because they disrupt the regularity of the α
helical backbone conformation.
• Alanine, glutamate, and leucine: α helices
• Valine & isoleucine: β strands.
• Glycine, asparagine, and proline: turns
34