Lec.1.Foundations of Biochemistry presentation.ppt
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About This Presentation
Introductory Biochemistry
Slide Content
Biochemistry
By
Haroon Amin
PhD Biochemistry (Scholar)
Certificate in Health Professions Education (CHPE)
By
Haroon Amin
PhD Biochemistry (Scholar)
Certificate in Health Professions Education (CHPE)
Learning Objectives
1. Understanding Basic Biochemical Concepts
•Comprehend the structure and function of biomolecules including
carbohydrates, proteins, lipids, and nucleic acids.
2. Metabolism and Energy Production
•Describe the pathways of carbohydrate metabolism, including
glycolysis, gluconeogenesis, and the citric acid cycle.
•Understand the process of oxidative phosphorylation and its role in ATP
production..
3. Clinical Relevance of Biochemical Pathways
•Relate biochemical pathways to clinical conditions, such as diabetes,
hyperlipidemia, and metabolic acidosis.
•Understand the biochemical basis of common laboratory tests, such as
liver function tests, renal function tests, and lipid profiles.
•Discuss the role of biochemical markers in the diagnosis and monitoring
of diseases.
1. Understanding Basic Biochemical Concepts
•Comprehend the structure and function of biomolecules including
carbohydrates, proteins, lipids, and nucleic acids.
2. Metabolism and Energy Production
•Describe the pathways of carbohydrate metabolism, including
glycolysis, gluconeogenesis, and the citric acid cycle.
•Understand the process of oxidative phosphorylation and its role in ATP
production..
3. Clinical Relevance of Biochemical Pathways
•Relate biochemical pathways to clinical conditions, such as diabetes,
hyperlipidemia, and metabolic acidosis.
•Understand the biochemical basis of common laboratory tests, such as
liver function tests, renal function tests, and lipid profiles.
•Discuss the role of biochemical markers in the diagnosis and monitoring
of diseases.
4. Biochemistry in Medical Imaging and Operation Theater
•Understand the biochemical basis of radiopharmaceuticals used in
imaging technology.
•Comprehend the biochemical aspects of anesthetics and their impact
on metabolism during surgical procedures.
5. Laboratory Techniques in Biochemistry
•Perform basic biochemical laboratory techniques, including
spectrophotometry, electrophoresis, and chromatography.
•Understand the principles behind laboratory assays used in clinical
biochemistry.
6. Integration of Biochemistry with Health Sciences
•Understand the importance of biochemistry in the context of health
sciences and its application in clinical settings.
•Integrate knowledge of biochemistry with other disciplines such as
physiology, pharmacology, and pathology.
•Develop critical thinking skills to apply biochemical concepts to
problem-solving in medical and surgical contexts.
•Understand the biochemical basis of radiopharmaceuticals used in
imaging technology.
•Comprehend the biochemical aspects of anesthetics and their impact
on metabolism during surgical procedures.
5. Laboratory Techniques in Biochemistry
•Perform basic biochemical laboratory techniques, including
spectrophotometry, electrophoresis, and chromatography.
•Understand the principles behind laboratory assays used in clinical
biochemistry.
6. Integration of Biochemistry with Health Sciences
•Understand the importance of biochemistry in the context of health
sciences and its application in clinical settings.
•Integrate knowledge of biochemistry with other disciplines such as
physiology, pharmacology, and pathology.
•Develop critical thinking skills to apply biochemical concepts to
problem-solving in medical and surgical contexts.
1. Bioelements
Definition: Bioelements are the chemical elements that are essential
for the structure and function of living organisms. These elements are
the building blocks of biomolecules and play crucial roles in various
biochemical processes.
The major Bioelements include carbon (C), hydrogen (H), oxygen (O),
nitrogen (N), phosphorus (P), and sulfur (S). These elements are
involved in the formation of organic molecules like proteins, lipids,
nucleic acids, and carbohydrates.
2. Biomolecules
Definition: Biomolecules are organic molecules that are produced by
living organisms and are essential for their structure, function, and
regulation. Biomolecules include a wide variety of molecules such as
carbohydrates, proteins, lipids, nucleic acids, and vitamins. They are
involved in various biological processes, such as energy production,
cellular structure, and the transmission of genetic information.
Definition: Bioelements are the chemical elements that are essential
for the structure and function of living organisms. These elements are
the building blocks of biomolecules and play crucial roles in various
biochemical processes.
The major Bioelements include carbon (C), hydrogen (H), oxygen (O),
nitrogen (N), phosphorus (P), and sulfur (S). These elements are
involved in the formation of organic molecules like proteins, lipids,
nucleic acids, and carbohydrates.
2. Biomolecules
Definition: Biomolecules are organic molecules that are produced by
living organisms and are essential for their structure, function, and
regulation. Biomolecules include a wide variety of molecules such as
carbohydrates, proteins, lipids, nucleic acids, and vitamins. They are
involved in various biological processes, such as energy production,
cellular structure, and the transmission of genetic information.
3. Organic Compounds
Definition: Organic compounds are chemical compounds that contain carbon
atoms bonded to hydrogen atoms and, in many cases, to other elements like
oxygen, nitrogen, sulfur, and phosphorus. These compounds are typically found
in living organisms and are central to the chemistry of life. Examples of organic
compounds include carbohydrates, proteins, lipids, and nucleic acids. Organic
compounds are characterized by their carbon-based structures, which allow for
a vast diversity of molecular forms and functions.
4. Inorganic Compounds
Definition: Inorganic compounds are chemical compounds that do not primarily
consist of carbon-hydrogen bonds. They include a wide range of substances
such as salts, minerals, metals, water, and gases like oxygen and carbon dioxide.
Inorganic compounds are essential for various physiological processes in living
organisms, such as ion transport, enzyme function, and the maintenance of pH
balance. Unlike organic compounds, inorganic compounds are not typically
associated with living organisms, although they play critical roles in biological
systems.
Definition: Organic compounds are chemical compounds that contain carbon
atoms bonded to hydrogen atoms and, in many cases, to other elements like
oxygen, nitrogen, sulfur, and phosphorus. These compounds are typically found
in living organisms and are central to the chemistry of life. Examples of organic
compounds include carbohydrates, proteins, lipids, and nucleic acids. Organic
compounds are characterized by their carbon-based structures, which allow for
a vast diversity of molecular forms and functions.
4. Inorganic Compounds
Definition: Inorganic compounds are chemical compounds that do not primarily
consist of carbon-hydrogen bonds. They include a wide range of substances
such as salts, minerals, metals, water, and gases like oxygen and carbon dioxide.
Inorganic compounds are essential for various physiological processes in living
organisms, such as ion transport, enzyme function, and the maintenance of pH
balance. Unlike organic compounds, inorganic compounds are not typically
associated with living organisms, although they play critical roles in biological
systems.
Foundation of Biochemistry
BIOCHEMISTRY
Biochemistry, sometimes called biological chemistry, is the study of
chemical processes within and relating to living organisms.
By controlling information flow through biochemical signaling and
the flow of chemical energy through metabolism, biochemical
processes give rise to the complexity of life.
Biochemistry, sometimes called biological chemistry, is the study of
chemical processes within and relating to living organisms.
By controlling information flow through biochemical signaling and
the flow of chemical energy through metabolism, biochemical
processes give rise to the complexity of life.
1. A high degree of chemical complexity and microscopic
organization.
2. Systems for extracting, transforming and using energy
from the environment.
3. A capacity for precise self-replication and self-assembly.
4. Mechanisms for sensing and responding to alterations
in their surroundings.
5. Defined functions for each of their components and
regulated interactions among them.
6. A history of evolutionary change.
Distinguishing Features of Living Organisms
organization.
2. Systems for extracting, transforming and using energy
from the environment.
3. A capacity for precise self-replication and self-assembly.
4. Mechanisms for sensing and responding to alterations
in their surroundings.
5. Defined functions for each of their components and
regulated interactions among them.
6. A history of evolutionary change.
Distinguishing Features of Living Organisms
Vertebrate muscle tissue viewed with EM
1. A high degree of chemical complexity and
microscopic organization.
1. A high degree of chemical complexity and
microscopic organization.
Falcon acquires nutrients by consuming a smaller bird
2. Systems for extracting, transforming, and
using energy from the environment.
2. Systems for extracting, transforming, and
using energy from the environment.
Biological reproduction occurs with near-perfect fidelity
3. A capacity for precise self-replication and
self-assembly.
3. A capacity for precise self-replication and
self-assembly.
4. Mechanisms for sensing and responding to
alterations in their surroundings.
5. Defined functions for each of their components and
regulated interactions among them.
Distinguishing Features of Living Organisms
alterations in their surroundings.
5. Defined functions for each of their components and
regulated interactions among them.
Distinguishing Features of Living Organisms
Diverse living organisms share common chemical features
6. A history of evolutionary
change.
6. A history of evolutionary
change.
Biochemistry describes in molecular terms the structures,
mechanisms, and chemical processes shared by all organisms
and provides organizing principles that underlie life in all its
diverse forms.
In this introductory section, the cellular, chemical, physical
(thermodynamic), genetic, and the evolutionary backgrounds to
biochemistry are described.
The Molecular Logic of Life
mechanisms, and chemical processes shared by all organisms
and provides organizing principles that underlie life in all its
diverse forms.
In this introductory section, the cellular, chemical, physical
(thermodynamic), genetic, and the evolutionary backgrounds to
biochemistry are described.
The Molecular Logic of Life
1.Cellular Foundations
2.Chemical Foundations
3.Physical Foundations
4.Genetic Foundations
5.Evolutionary Foundations
The Foundations of Biochemistry
2.Chemical Foundations
3.Physical Foundations
4.Genetic Foundations
5.Evolutionary Foundations
The Foundations of Biochemistry
1. Cells are the structural and functional units of all living
organisms.
2. Cellular dimensions are limited by oxygen diffusion.
3. There are three distinct domains of life.
4. Escherichia coli is the most-studied prokaryotic cell.
5. Eukaryotic cells have a variety of membranous organelles,
which can be isolated for study.
6. The cytoplasm is organized by the cytoskeleton and is
highly dynamic.
7. Cells build supramolecular structures.
Cellular Foundations
organisms.
2. Cellular dimensions are limited by oxygen diffusion.
3. There are three distinct domains of life.
4. Escherichia coli is the most-studied prokaryotic cell.
5. Eukaryotic cells have a variety of membranous organelles,
which can be isolated for study.
6. The cytoplasm is organized by the cytoskeleton and is
highly dynamic.
7. Cells build supramolecular structures.
Cellular Foundations
The universal features of living cells
1. Cells are the structural and functional units of
all living organisms.
1. Cells are the structural and functional units of
all living organisms.
Animal and plant cells – 5-100 m in diameter
Bacteria – 1-2 m long
What limits the dimension of a cell?
2. Cellular dimensions are limited by oxygen diffusion.
Lower limit – minimum number of each type of
biomolecules required by the cell.
Upper limit – rate of diffusion of solute molecules in
aqueous systems (ex: oxygen).
Bacteria – 1-2 m long
What limits the dimension of a cell?
2. Cellular dimensions are limited by oxygen diffusion.
Lower limit – minimum number of each type of
biomolecules required by the cell.
Upper limit – rate of diffusion of solute molecules in
aqueous systems (ex: oxygen).
3. There are three distinct domains of life.
Organisms can be classified according to their source of
energy and carbon for the synthesis of cellular material
energy and carbon for the synthesis of cellular material
Common structural features of bacterial cells
4. Escherichia coli is the most-studied prokaryotic cell.
4. Escherichia coli is the most-studied prokaryotic cell.
Common structural features of bacterial cells
5. Eukaryotic cells have a variety of membranous
organelles, which can be isolated for study.
organelles, which can be isolated for study.
5. Eukaryotic cells have a variety of membranous
organelles, which can be isolated for study.
organelles, which can be isolated for study.
Subcellular fractionation of tissue –
Differential centrifugation
Differential centrifugation
Subcellular fractionation of tissue –
Isopycnic (sucrose density) centrifugation
Isopycnic (sucrose density) centrifugation
The three types of cytoskeletal filaments
6. The cytoplasm is organized by the
cytoskeleton and is highly dynamic.
6. The cytoplasm is organized by the
cytoskeleton and is highly dynamic.
7. Cells build supramolecular structures.
The organic compounds from which most cellular
materials are constructed: the ABCs of biochemistry
materials are constructed: the ABCs of biochemistry
The organic compounds from which most cellular
materials are constructed: the ABCs of biochemistry
materials are constructed: the ABCs of biochemistry
Structural hierarchy in the molecular organization of cells
Covalent bonds
The monomeric subunits in
proteins, nucleic acids, and
polysaccharides are joined
by covalent bonds.
The monomeric subunits in
proteins, nucleic acids, and
polysaccharides are joined
by covalent bonds.
In supramolecular complexes, macromolecules are held
together by noncovalent interactions – much weaker,
individually, than covalent bonds.
Noncovalent interactions:
(1) Hydrogen bonds (between polar groups)
(2) Ionic interactions (between charged groups)
(3) Hydrophobic interactions (among nonpolar groups)
(4) van der Waals interactions
Noncovalent interactions
together by noncovalent interactions – much weaker,
individually, than covalent bonds.
Noncovalent interactions:
(1) Hydrogen bonds (between polar groups)
(2) Ionic interactions (between charged groups)
(3) Hydrophobic interactions (among nonpolar groups)
(4) van der Waals interactions
Noncovalent interactions
1.Cellular Foundations
2.Chemical Foundations
3.Physical Foundations
4.Genetic Foundations
5.Evolutionary Foundations
The Foundations of Biochemistry
2.Chemical Foundations
3.Physical Foundations
4.Genetic Foundations
5.Evolutionary Foundations
The Foundations of Biochemistry
Antoine Lavoisier (1743-1794) noted the relative chemical
simplicity of the “mineral world” and contrasted it with the
complexity of the “plant and animal worlds”, which were
composed of compounds rich in the elements carbon,
oxygen, nitrogen, and phosphorus.
Jacques Monod: “What is true of E. coli is true of the elephant.”
Only about 30 of the more than 90 naturally occurring chemical
elements are essential to organisms.
Chemical Foundations
simplicity of the “mineral world” and contrasted it with the
complexity of the “plant and animal worlds”, which were
composed of compounds rich in the elements carbon,
oxygen, nitrogen, and phosphorus.
Jacques Monod: “What is true of E. coli is true of the elephant.”
Only about 30 of the more than 90 naturally occurring chemical
elements are essential to organisms.
Chemical Foundations
Elements essential to animal life and health
1. Biomolecules are compounds of carbon with a
variety of functional groups.
2. Cells contain a universal set of small molecules.
3. Macromolecules are the major constituents of
cells.
4. Three-dimensional structure is described by
configuration and conformation.
5. Interactions between biomolecules are
stereospecific.
Chemical Foundations
variety of functional groups.
2. Cells contain a universal set of small molecules.
3. Macromolecules are the major constituents of
cells.
4. Three-dimensional structure is described by
configuration and conformation.
5. Interactions between biomolecules are
stereospecific.
Chemical Foundations
Versatility of carbon bonding
1. Biomolecules are compounds of carbon
with a variety of functional groups.
1. Biomolecules are compounds of carbon
with a variety of functional groups.
Geometry of carbon bonding
Some common functional groups of biomolecules (1)
Some common functional groups of biomolecules (2)
Some common functional groups of biomolecules (3)
Some common functional groups of biomolecules (4)
Some common functional groups of biomolecules (5)
Several common functional groups in a single biomolecule
In cytosol, there exists a collection of 100-200 different small
organic molecules (M
r ~100 to ~500), including the common
amino acids, nucleotides, sugars and their phosphorylated
derivatives, and a number of mono-, di-, and tricarboxylic acids.
The molecules are polar or charged, water soluble, and present in
M to mM concentrations.
Secondary metabolites: morphine, quinine, nicotine, caffeine, etc.
“Metabolome” – the entire collection of small molecules in a give
cell.
2. Cells contain a universal set of small molecules.
organic molecules (M
r ~100 to ~500), including the common
amino acids, nucleotides, sugars and their phosphorylated
derivatives, and a number of mono-, di-, and tricarboxylic acids.
The molecules are polar or charged, water soluble, and present in
M to mM concentrations.
Secondary metabolites: morphine, quinine, nicotine, caffeine, etc.
“Metabolome” – the entire collection of small molecules in a give
cell.
2. Cells contain a universal set of small molecules.
Molecular weight, relative molecular mass (M
r) – the ratio of the
mass of a molecule to 1/12 the mass of
12
C.
M
r
is a ratio, it is dimensionless and has no associated units.
Molecular mass (m) – the mass of one molecule ; the molecular
mass divided by Avogadro’s number.
m is expressed in daltons (Da).
One dalton is equivalent to 1/12 the mass of
12
C.
Kilodalton (kDa): 1000 Da ; megadalton (MDa): 10
6
Da.
Atomic mass unit (amu, u) – 1 u is 1/12 the mass of an atom of
12
C. (1.66 x 10
-24
g)
Molecular weight, molecular mass, and their correct units
r) – the ratio of the
mass of a molecule to 1/12 the mass of
12
C.
M
r
is a ratio, it is dimensionless and has no associated units.
Molecular mass (m) – the mass of one molecule ; the molecular
mass divided by Avogadro’s number.
m is expressed in daltons (Da).
One dalton is equivalent to 1/12 the mass of
12
C.
Kilodalton (kDa): 1000 Da ; megadalton (MDa): 10
6
Da.
Atomic mass unit (amu, u) – 1 u is 1/12 the mass of an atom of
12
C. (1.66 x 10
-24
g)
Molecular weight, molecular mass, and their correct units
Proteins – enzymes (catalysis) ; structural elements ; signal
receptors ; transporters…etc.
Nucleic acids – DNA and RNA, store and transmit genetic
information ; some RNAs have structural and catalytic roles.
Polysaccharides – energy-yielding fuel stores ; extracellular
structural elements with specific binding sites ; specific
cellular signals.
Lipids – structural components of membranes ; energy-rich fuel
stores ; pigments ; intracellular signals.
3. Macromolecules are the major constituents of cells.
receptors ; transporters…etc.
Nucleic acids – DNA and RNA, store and transmit genetic
information ; some RNAs have structural and catalytic roles.
Polysaccharides – energy-yielding fuel stores ; extracellular
structural elements with specific binding sites ; specific
cellular signals.
Lipids – structural components of membranes ; energy-rich fuel
stores ; pigments ; intracellular signals.
3. Macromolecules are the major constituents of cells.
Major classes of biomolecules in the bacterium E. coli
Representations of molecules
4. Three-dimensional structure is described
by configuration and conformation.
4. Three-dimensional structure is described
by configuration and conformation.
Configurations of geometric (cis-trans) isomers (1)
Configurations of geometric (cis-trans) isomers (2)
Molecular asymmetry – chiral and achiral molecules
Two types of stereoisomers – enantiomers and diastereomers
The RS and DL system for nomenclature in stereochemistry
The priorities of some common substituents attached to the
chiral carbon:
-OCH
2
＞ -OH ＞ -NH
2
＞ -COOH ＞ -CHO ＞
-CH
2
OH ＞ -CH
2
＞ -H
The priorities of some common substituents attached to the
chiral carbon:
-OCH
2
＞ -OH ＞ -NH
2
＞ -COOH ＞ -CHO ＞
-CH
2
OH ＞ -CH
2
＞ -H
Louis Pasteur and optical activity
In 1843, Louis Pasteur discovered optical activity
during his investigation of the crystalline sediment
accumulated in wine casks (paratartaric acid,
racemic acid). He used fine forceps to separate
two types of crystals indentical in shapes but
mirror images of each other.
Louis Pasteur
In 1843, Louis Pasteur discovered optical activity
during his investigation of the crystalline sediment
accumulated in wine casks (paratartaric acid,
racemic acid). He used fine forceps to separate
two types of crystals indentical in shapes but
mirror images of each other.
Louis Pasteur
Conformations – the staggered and the eclipsed
Eclipsed –
least stable
Staggered –
more stable
Eclipsed –
least stable
Staggered –
more stable
Complementary fit between a macromolecule and a small molecule
RNA segment of the HIV genome
A bound argininamide molecule
5. Interactions between biomolecules are stereospecific.
RNA segment of the HIV genome
A bound argininamide molecule
5. Interactions between biomolecules are stereospecific.
Stereoisomers distinguishable by smell in humans
Stereoisomers distinguishable by taste in humans
1. Changes in the hereditary instructions allow evolution.
2. Biomolecules first arose by chemical evolution.
3. Chemical evolution can be simulated in the laboratory.
4. RNA or related precursors may have been the first genes and
catalysts.
5. Biological evolution began more than three and a half billion
years ago.
6. The first cell was probably a chemoheterotroph.
7. Eukaryotic cells evolved from prokaryotes in several stages.
8. Molecular anatomy reveals evolutionary relationships.
9. Functional genomics shows the allocations of genes to
specific cellular processes.
10. Genomic comparisons will have increasing importance in
human biology and medicine.
Evolutionary Foundations
2. Biomolecules first arose by chemical evolution.
3. Chemical evolution can be simulated in the laboratory.
4. RNA or related precursors may have been the first genes and
catalysts.
5. Biological evolution began more than three and a half billion
years ago.
6. The first cell was probably a chemoheterotroph.
7. Eukaryotic cells evolved from prokaryotes in several stages.
8. Molecular anatomy reveals evolutionary relationships.
9. Functional genomics shows the allocations of genes to
specific cellular processes.
10. Genomic comparisons will have increasing importance in
human biology and medicine.
Evolutionary Foundations
Landmarks in the evolution
of life on Earth
of life on Earth
Evolution of eukaryotes through endosymbiosis
Comparison of prokaryotic and eukaryotic cells
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