The document provides an overview of a biochemistry course for 3rd year biology majors. It includes information about the course title, code, credit hours, evaluation criteria, and course outline. The course outline covers topics such as the introduction to biochemistry, chemistry of amino acids and proteins, enzymes, carbohydrates, and lipids. The document also defines biochemistry and discusses the scope and importance of studying biochemistry. It explains key cellular components and organelles, including their structures and functions. Additionally, it summarizes important concepts around water properties, chemical bonds, and biological buffer systems.
the branch of science concerned with the chemical and physico-chemical processes and substances that occur within living organisms.
the processes and substances with which the science of biochemistry is concerned.
the branch of science concerned with the chemical and physico-chemical processes and substances that occur within living organisms.
the processes and substances with which the science of biochemistry is concerned.
Introduction to Biochemistry and Clinical PathologyDHANANJAY PATIL
A brief introduction to the subject of biochemistry and clinical pathology. This introduction will give readers a quick overall view of this subject. All types of queries and suggestions are most welcome.
The science concerned with the materials and various processes of life related to chemical basis of life.
The science concerned with the various molecules that occur in living cells and organisms and with their chemical reaction
ubio is starting a series of biology tutorials aimed at introducing biology, biotechnology and bioinformatics to computer engineers. The first part of the presentation is essentially a biochemistry tutorial that introduces molecular biochemistry.
What is biochemistry?
Biochemistry explores chemical processes related to living organisms. It is a laboratory-based science combining biology and chemistry.
Biochemists study the structure, composition, and chemical reactions of substances in living systems and, in turn, their functions and ways to control them. Biochemistry emerged as a separate discipline when scientists combined biology with organic, inorganic, and physical chemistry. They began to study areas such as:
How living things get energy from food
The chemical basis of heredity
What fundamental changes occur in disease
Biochemistry includes the sciences of molecular biology, immunochemistry, and neurochemistry, as well as bioinorganic, bioorganic, and biophysical chemistry.
What do biochemists do?
Biochemists interact with scientists from a wide variety of other disciplines, usually on problems that are a very small piece of a very large and complex system.
Biochemists in industry are interested in specific applications that will lead to marketable products
Biochemists in academia or government labs conduct more basic and less applied research
Where is biochemistry used?
Biochemistry has obvious applications in medicine, dentistry, and veterinary medicine. Other applications include:
Food Science
Biochemists determine the chemical composition of foods, research ways to develop abundant and inexpensive sources of nutritious foods, develop methods to extract nutrients from waste products, and/or invent ways to prolong the shelf life of food products.
Agriculture
Biochemists study the interaction of herbicides/insecticides with plants and pests. They examine the structure–activity relationships of compounds, determine their ability to inhibit growth, and evaluate the toxicological effects on surrounding life.
Pharmacology, Physiology, Microbiology, Toxicology, and Clinical Chemistry
Biochemists investigate the mechanisms of drug actions; engage in viral research; conduct research pertaining to organ function; or use chemical concepts, procedures, and techniques to study the diagnosis and therapy of disease and the assessment of health.
the branch of science concerned with the chemical and physico-chemical processes and substances that occur within living organisms.
the processes and substances with which the science of biochemistry is concerned.
Introduction to Biochemistry and Clinical PathologyDHANANJAY PATIL
A brief introduction to the subject of biochemistry and clinical pathology. This introduction will give readers a quick overall view of this subject. All types of queries and suggestions are most welcome.
The science concerned with the materials and various processes of life related to chemical basis of life.
The science concerned with the various molecules that occur in living cells and organisms and with their chemical reaction
ubio is starting a series of biology tutorials aimed at introducing biology, biotechnology and bioinformatics to computer engineers. The first part of the presentation is essentially a biochemistry tutorial that introduces molecular biochemistry.
What is biochemistry?
Biochemistry explores chemical processes related to living organisms. It is a laboratory-based science combining biology and chemistry.
Biochemists study the structure, composition, and chemical reactions of substances in living systems and, in turn, their functions and ways to control them. Biochemistry emerged as a separate discipline when scientists combined biology with organic, inorganic, and physical chemistry. They began to study areas such as:
How living things get energy from food
The chemical basis of heredity
What fundamental changes occur in disease
Biochemistry includes the sciences of molecular biology, immunochemistry, and neurochemistry, as well as bioinorganic, bioorganic, and biophysical chemistry.
What do biochemists do?
Biochemists interact with scientists from a wide variety of other disciplines, usually on problems that are a very small piece of a very large and complex system.
Biochemists in industry are interested in specific applications that will lead to marketable products
Biochemists in academia or government labs conduct more basic and less applied research
Where is biochemistry used?
Biochemistry has obvious applications in medicine, dentistry, and veterinary medicine. Other applications include:
Food Science
Biochemists determine the chemical composition of foods, research ways to develop abundant and inexpensive sources of nutritious foods, develop methods to extract nutrients from waste products, and/or invent ways to prolong the shelf life of food products.
Agriculture
Biochemists study the interaction of herbicides/insecticides with plants and pests. They examine the structure–activity relationships of compounds, determine their ability to inhibit growth, and evaluate the toxicological effects on surrounding life.
Pharmacology, Physiology, Microbiology, Toxicology, and Clinical Chemistry
Biochemists investigate the mechanisms of drug actions; engage in viral research; conduct research pertaining to organ function; or use chemical concepts, procedures, and techniques to study the diagnosis and therapy of disease and the assessment of health.
the branch of science concerned with the chemical and physico-chemical processes and substances that occur within living organisms.
the processes and substances with which the science of biochemistry is concerned.
Biochemistry, sometimes called biological chemistry, is the study of chemical processes within and relating to living organisms.[1] Biochemical processes give rise to the complexity of life.
Biochemistry is the study of the chemical substances and vital processes occurring in living organisms. Biochemists focus heavily on the role, function, and structure of biomolecules. The study of the chemistry behind biological processes and the synthesis of biologically active molecules are examples of biochemistry.
“Foundations of Biochemistry” is a process‐oriented guided inquiry learning (POGIL) style workbook for use in upper division Biochemistry courses. The book contains 36 exercises, which could be used for an almost‐exclusively POGIL one semester course or supplemented with lectures, case studies, or student presentations for a full year course. It is intended as a supplement to a textbook, and the very modest price makes it a very cost‐effective educational resource.
Embracing GenAI - A Strategic ImperativePeter Windle
Artificial Intelligence (AI) technologies such as Generative AI, Image Generators and Large Language Models have had a dramatic impact on teaching, learning and assessment over the past 18 months. The most immediate threat AI posed was to Academic Integrity with Higher Education Institutes (HEIs) focusing their efforts on combating the use of GenAI in assessment. Guidelines were developed for staff and students, policies put in place too. Innovative educators have forged paths in the use of Generative AI for teaching, learning and assessments leading to pockets of transformation springing up across HEIs, often with little or no top-down guidance, support or direction.
This Gasta posits a strategic approach to integrating AI into HEIs to prepare staff, students and the curriculum for an evolving world and workplace. We will highlight the advantages of working with these technologies beyond the realm of teaching, learning and assessment by considering prompt engineering skills, industry impact, curriculum changes, and the need for staff upskilling. In contrast, not engaging strategically with Generative AI poses risks, including falling behind peers, missed opportunities and failing to ensure our graduates remain employable. The rapid evolution of AI technologies necessitates a proactive and strategic approach if we are to remain relevant.
Francesca Gottschalk - How can education support child empowerment.pptxEduSkills OECD
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Honest Reviews of Tim Han LMA Course Program.pptxtimhan337
Personal development courses are widely available today, with each one promising life-changing outcomes. Tim Han’s Life Mastery Achievers (LMA) Course has drawn a lot of interest. In addition to offering my frank assessment of Success Insider’s LMA Course, this piece examines the course’s effects via a variety of Tim Han LMA course reviews and Success Insider comments.
Palestine last event orientationfvgnh .pptxRaedMohamed3
An EFL lesson about the current events in Palestine. It is intended to be for intermediate students who wish to increase their listening skills through a short lesson in power point.
2024.06.01 Introducing a competency framework for languag learning materials ...Sandy Millin
http://sandymillin.wordpress.com/iateflwebinar2024
Published classroom materials form the basis of syllabuses, drive teacher professional development, and have a potentially huge influence on learners, teachers and education systems. All teachers also create their own materials, whether a few sentences on a blackboard, a highly-structured fully-realised online course, or anything in between. Despite this, the knowledge and skills needed to create effective language learning materials are rarely part of teacher training, and are mostly learnt by trial and error.
Knowledge and skills frameworks, generally called competency frameworks, for ELT teachers, trainers and managers have existed for a few years now. However, until I created one for my MA dissertation, there wasn’t one drawing together what we need to know and do to be able to effectively produce language learning materials.
This webinar will introduce you to my framework, highlighting the key competencies I identified from my research. It will also show how anybody involved in language teaching (any language, not just English!), teacher training, managing schools or developing language learning materials can benefit from using the framework.
Operation “Blue Star” is the only event in the history of Independent India where the state went into war with its own people. Even after about 40 years it is not clear if it was culmination of states anger over people of the region, a political game of power or start of dictatorial chapter in the democratic setup.
The people of Punjab felt alienated from main stream due to denial of their just demands during a long democratic struggle since independence. As it happen all over the word, it led to militant struggle with great loss of lives of military, police and civilian personnel. Killing of Indira Gandhi and massacre of innocent Sikhs in Delhi and other India cities was also associated with this movement.
Synthetic Fiber Construction in lab .pptxPavel ( NSTU)
Synthetic fiber production is a fascinating and complex field that blends chemistry, engineering, and environmental science. By understanding these aspects, students can gain a comprehensive view of synthetic fiber production, its impact on society and the environment, and the potential for future innovations. Synthetic fibers play a crucial role in modern society, impacting various aspects of daily life, industry, and the environment. ynthetic fibers are integral to modern life, offering a range of benefits from cost-effectiveness and versatility to innovative applications and performance characteristics. While they pose environmental challenges, ongoing research and development aim to create more sustainable and eco-friendly alternatives. Understanding the importance of synthetic fibers helps in appreciating their role in the economy, industry, and daily life, while also emphasizing the need for sustainable practices and innovation.
3. Course Outline
1.Introduction
♣ Definition and Scope of Biochemistry
♣ The Cell and its organelles
♣ Water and Chemical bonds in biochemistry
♣ pH and biological buffer ring systems
2.Chemistry of Amino acids and Proteins
3.Enzymes
4.Chemistry of Carbohydrates
5.Metabolism of Carbohydrates
6. Chemistry of Lipids
7. Metabolism of lipid
3
4. Definition Biochemistry
Definition :
The Simplest definition: Biochemistry is “Chemistry of the living cell”
The science that study about the chemical constituents of living cells and the
reactions and processes they undergo
It is essential to understand basic functions in the body
Why do we study Biochemistry?
We study biochemistry to understand:
♣ the chemical processes that take place in living organisms
♣ the chemical logic of living things includes synthesis and degradation of
small organic molecules
♣ How energy is formed during chemical reaction and their transformation
♣ important issues in medicine, health, and nutrition 4
5. Scope of Biochemistry
The term ‘Biochemistry’ was first introduced by the German
Chemist Carl Neuberg in 1903.
Biochemistry takes into account the studies related to:
the nature of the chemical constituents of living matter,
their transformations in biological systems and
the energy changes associated with these transformations
Biochemistry is related to all of the other sciences that study about
living organisms
E.g. molecular biology, molecular genetics, physiology, toxicology,
drug design, nutrition….
Many newer disciplines have been emerged from biochemistry such
as:
enzymology (study of enzymes),
endocrinology (study of hormones),
clinical biochemistry (study of diseases), 5
6. Cellular Organization
All cell similarities:
Use energy (ATP)
Cells structure and function
Biomolecular organization
The cell has three major components:
1. The cell membrane/plasma membrane = composed of a
phospholipids lipid bilayer in which proteins are embedded; hence the
name fluid mosaic membrane.
It limits the size of the cell and
Controls transport of materials in and out of the cell.
It is partially permeable and highly regulatory.
2. The Cytoplasm = contains the cellular organelles suspended in a jelly
like fluid called the cytosol
3. Nucleus = has nuclear envelop that separates it from the cytoplasm. It
contains the nucleoplasm (DNA, RNA and proteins).
6
8. The cellular organelles
1) Mitochondria
Mitochondria (Greek: ‘mitos’-thread;
‘chondros’-granule)
the power generators/ ATP production
Surrounded by a double membrane
with a series of folds called cristae.
Contains its own DNA.
The outer and inner mitochondrial
membranes, that separate the matrix
from the cytosol.
8
9. Mitochondria…
The outer membrane contains pores made of the protein porin and is
freely permeable to most ions and small molecules.
Where as the inner membrane is a specialized structure that is highly
impermeable to charged substances (H+, Na+, and K+ )
Transport across inner mitochondrial membrane requires special
carrier proteins.
Inner mitochondrial membrane is unusually rich in proteins b/c it is the
site of electron transport chain and oxidative phosphorylation.
It forms convolutions known as cristae that greatly increase its surface
area.
The mitochondrial matrix:
gel-like solution in the interior of mitochondria 50% protein
(most of them are enzymes).
9
10. 2) Endoplasmic reticulum (ER): is a network of membranous
tubules within the cell.
♣ Rough ER – studded (associated) with ribosomes and hence
serves as site of protein synthesis.
♣ Smooth ER - lacks ribosome. It has role in lipid and steroid
hormone synthesis, detoxification, glycogen storage.
3) Ribosomes: are nucleoproteins (made of ribosomal proteins and
nucleic acids). They are just supramolecular structures.
♣ Present either attached on RER or free in the cytosol.
♣ They serve as site of protein synthesis in both cases.
10
11. 4) Golgi apparatus – ‘post office’
♣It consists of a curved stack of flattened vesicles called
cisternae.
♣involved in modifying, sorting, and distributing proteins
produced in the RER to lysosomes, secretory vesicles or to
the plasma membrane.
5) Lysosomes – suicide bag/sac
Contain hydrolytic enzymes and are involved in intracellular
digestion.
Involved in digestion and elimination of unwanted material
11
12. 6) Peroxisomes
Involved in oxidative reactions using O2 such as in oxidation of
very long chain fatty acids (>or=20 carbons) to shorter chain
fatty acids, conversion of cholesterol to bile acids…
These reactions produce H2O2, which is toxic hence used or
degraded by catalase
12
13. 7. Cytoskeleton
It is a flexible fibrous protein support the cell
composed of three types of fibrous protein components:
♣ Microtubules composed of tubulin - move and position organelles
and vesicles
♣ Thin filaments (actin microfilaments) composed of actin, form
cytoskeleton
♣ Intermediate filaments composed of different fibrous proteins
such as α-keratin
Roles of the cytoskeleton include:
maintains structure or shape of the cell surface,
fixes the position of organelles
moves compounds within the cell or moves the cell itself 13
17. Water
Water is the most abundant substance in living systems, making up
~ 70% of weight of most organisms.
Biological importance of water in living things
the transport of nutrients in blood, removal of wastes
the site of enzyme catalyzed reactions (chemical rxn)
the transfer of chemical energy occur
Regulation of body temp
Maintain the structure and function of biomolecules
Dissolves ionic and polar molecules, universal solvent
Two properties of water are especially important biologically:
1) its polar nature
2) the strong cohesive forces (hydrogen bonding capability)
between water molecules.
17
18. The polar nature
The water molecule has a polar structure
with two lone pair electrons on the oxygen
atom.
The oxygen nucleus draws electrons away
from the hydrogen nuclei, which leaves the
region around the hydrogen nuclei with a net
positive charge making the molecule polar.
The cohesive forces
Due to its polar nature water molecules
interact strongly with one another through
hydrogen bonds.
18
19. The cohesive forces
In a solid state (in ice) each water
molecule forms four hydrogen bonds
with the surrounding four water
molecules and networks of hydrogen
bonds hold the structure together.
Whereas in a liquid state each water
molecule forms less number of
hydrogen bonds because some of them
broken down as it changes from solid to
liquid state.
19
20. unusual (unique) physical properties of water are:
♣ high surface tension (force acting to push together the liquid
molecules)
allow water to serve as transport medium
♣ high heat of vaporization (amount of heat needed to convert liquid to
gas phase)
helps to keep body temperature constant
♣ Water Expand upon freezing
density decrease as it cools down (max density at 4degree
centigrade)
allow organisms to live at the bottom of fresh water lakes, protected
from freezing and for ease melting
♣ has high solvent power
Water is a powerful dissolver of ions & polar compounds & similarly powerful
excluder non-polar molecules
♣ high specific heat capacity that makes it serve as a heat buffer
♣ high melting point and boiling point
20
21. Chemical Bonds in Biomolecules
Living organisms are composed of organic molecules referred to
as biomolecules.
The major ones are:
Proteins,
Carbohydrates,
Lipids and
Nucleic acids (RNA and DNA).
Molecular interactions among biomolecules is mediated by two
general types of chemical bonds:
i) Covalent bonds and
ii) Non covalent interactions
Major d/c is the bond energy (a single covalent bond is far much
strong compared to a single non - covalent bond).
21
22. Covalent bonds are true chemical bonds present in biomolecules
is formed by the sharing of a pair of electrons between
adjacent atoms.
Important covalent bonds in biomolecules include:
Peptide bonds = b/n amino acids in proteins
Glycosidic bonds = b/n monosacharides in oligo and
polysaccharides and
Ester bonds in fats
Phosphodiester bonds b/n nucleotides in DNA and RNA.
Because of the dynamic nature of chemical processes occurring
in living cells; readily reversible, non-covalent molecular
interactions are crucial.
Although non - covalent bonds are individually weak, collectively
these bonds have a very significant role in stabilizing the
structures of proteins, nucleic acids, polysaccharides and
supramolecular structures like membrane lipids and ribosomes.
22
23. Such weak, non-covalent forces are also the key means by which
molecules interact with one another:
hormones - receptors,
antibodies - antigens.
in the replication of DNA,
the folding of proteins into three-dimensional forms,
the specific recognition of substrates by enzymes, and the
detection of molecular signals
There are four non covalent weak interactions (2dry ) that mediate
the reversible dynamic interaction of biomolecules:
hydrogen bond,
electrostatic interaction (ionic bond or salt bridge),
hydrophobic interaction and
Vander waals interaction.
23
24. i) Electrostatic interactions - are formed by electrostatic attraction
between two oppositely charged ions.
In living cells, there are a number of ionizable chemical entities
that bear a positive (e.g., amino, R–NH3
+) or a negative (e.g.,
carboxylic, R–COO-, -PO4
-) charge.
ii) Hydrogen bonds - are formed between an electronegative atom
(usually oxygen or nitrogen) and a hydrogen atom covalently
bonded to another electronegative atom in the same or another
molecule.
Hence the H atom in a H-bond is partly shared between two
relatively electronegative atoms.
Therefore H- bond is represented by broken lines
24
25. iii) Van der Waals interactions - are formed b/n any two atoms in
close proximity within a molecule.
They are formed due to charge asymmetry around an atom due to
asymmetric distribution of electronic charge.
This charge asymmetry around an atom in turn acts through
electrostatic interactions to induce a complementary charge
asymmetry in the electron distribution around its neighboring
atoms.
iv) Hydrophobic interaction - Based on their interaction with water
biomolecules can be classified as:
Hydrophilic,
Hydrophobic
Amphipathic
25
27. Hydrophilic - dissolve readily in water because they can replace
energetically favorable water-water interactions with even more
favorable water-solute interactions. E.g. polar molecule
Hydrophobic - poorly soluble/ insoluble in water b /c it
interferes with favorable water-water interactions and decrease
entropy of the system . E.g., non-polar molecule
Therefore in aqueous solutions, hydrophobic molecules tend to
cluster together to minimize the energetically unfavorable effects
of their presence .
This interaction of non-polar biomolecules in aqueous
environment is referred to as hydrophobic interaction
27
28. An amphipathic compound - contains both polar and non-
polar regions.
The polar or charged, hydrophilic region interact favorably with
the solvent and tends to dissolve, but non-polar, the hydrophobic
region has the opposite tendency, to avoid contact with water
(hydrophobic interaction).
Hydrophobic interaction is particularly important in biological
membranes by stabilizing its component amphipathic . e.g.
phospholipids bilayer.
28
30. Biological buffer systems
Buffers:
are a solution of weak acid and base that resists a significant change in
pH upon addition of an acid or a base.
are mixtures of weak acids and their conjugate bases.
Buffers tend to resist changes in pH when small amounts of acids or bases
added.
weak acids and bases are weak electrolytes and dissociate in aqueous
solution very slightly and they exist in a state of equilibrium in the body.
Ex. mixture of CH3COOH (proton donor) and CH3COO- (proton acceptor)
in dissociation of acetic acid.
This property of weak acids and bases play an important role in
maintenance of the physiologic pH by serving as buffers.
30
31. The buffering tendency of any weak acid/base conjugate is
determined by its pKa (dissociation constant)
pKa- is defined as the appropriate pH at which a given acid shows
maximum dissociation
Weak acids on the other hand, exhibit a 50% dissociation at their
appropriate pH and hence have generally a lower pKa value.
The relationship between pH, pKa and the molar ratio of the
acid/base conjugate in a solution is determined as follows according
to the Henderson -Hasselbalch equation.
Equilibrium of any weak acid
Where HA - represents a weak acid
A- “ conjugate base
K1- “ rate constant for dissociation of the acid
K2- represents the rate constant for association of the
conjugate base and H+ 31
32. The equilibrium constant, Ka for the weak acid(HA) is defined
by the following equation
Equation1
The equation can be rearranged to define [ H+] as follows
Equation 2
The [ H+] is often reported as pH, which is –log [H+].
In a similar fashion, -log Ka is represented by pKa.
Equation 2 can be converted to the negative (-log) form by
substituting pH and pKa:pH= pKa + log[ A-] Equation -3
[HA]
32
33. Equation 3- is the familiar henderson-Hasselbalch equation,
which defines the relation ship between pH, pKa and the ratio
of acid and conjugate base concentrations.
pH= pKa+ log [ A-]
[HA]
The buffering capacity of a buffer system is best when pKa of an
acid is equal to the pH of the medium.
[A-] = [HA], such that the ratio of [A-]/ HA] is 1 so pH =
pKa
This occurs when [proton donor] = [proton acceptor].
Therefore a buffer system with pKa value close to the
physiological pH =7.4 is a good extracellular (blood plasma)
buffer system.
E.g. acetic acid/acetate conjugate is not a good buffer system in
blood because the pKa of acetic acid 4.75 is far from 7.4.
33
34. In mammals (including man) the important buffer systems are:
the bicarbonate buffer system,
the phosphate buffer system and
the amino acid and protein buffer systems
1. The bicarbonate buffer system
It is the major buffer system in blood plasma; consists of
carbonic acid (H2CO3) and its conjugate base bicarbonate ion
(HCO3
-).
The Henderson-Hasselbalch equation for this conjugate be:
pH = pKa + log [HCO3
-]/[H2CO3].
However, ~99 parts of 100 molecules of H2CO3 in aqueous
solution are formed from CO2 dissolved in water.
The rxn take place in RBCs catalyzed by carbnonic anhydrase.
Therefore, in the blood, [CO2] is approximately equal to [H2CO3].
34
35. Thus The H-H equation can be rewritten as: pH = pKa + log
[HCO3
-]/[CO2].
From this equation, we can deduce; In body fluids, pH increases
with the increase in [HCO3
-] but decreases as [CO2] increases.
The bicarbonate buffer looks a weak buffer system in the blood
because:
pKa of H2CO3 , 6.1 is relatively far from 7.4.
In addition [CO2] & [HCO3
-] in the blood are low or limited.
However, these concentrations are regulated by lung and kidney
respectively making the bicarbonate buffer an important system
in the blood plasma.
35
36. 2. Phosphate buffer system
It involves the dissociation of phosphoric acid which has three
ionizable hydrogen atoms:
H3PO4 ↔ H+ + H2PO4
- pKa = 2.0
H2PO4
- ↔ H+ + HPO4
2- pKa = 6.8
HPO4
2- ↔ H+ + PO4
3- pKa = 12.7
Q. Which one do you think would be the best buffer system in the
blood and why?
The second is an important buffer in our body b/se 6.8 is very
close to 7.4.
Phosphate buffer is primarily important intracellular particularly
in kidneys and in urine where their concentration is higher.
36
38. Amino Acids
Amino acids are the simplest building blocks of proteins.
The word protein comes from the Greek word ‘proteos’ meaning
“primary/ 1st ”
The most abundant and important class of organic compounds in
our body, constituting more than half of its cellular dry weight
Although more than 300 different amino acids have been
described in nature, only 20 are commonly found as constituents
of proteins in living things.
These are (20) the only amino acids that are coded for by
DNA; the genetic material in the cell.
38
39. Structure of amino acids
Each amino acid has an hydrogen
atom, a carboxyl group, a primary
amino group, and a distinctive side
chain or radical (“R-group”) bonded
to the α-carbon atom.
Amino acids have carboxyl and amino
groups bonded to the α-carbon atom-
called α-amino acids
The side chain or R - group
distinguishes each amino acid
chemically
All amino acids except proline do have
the structure shown in the figure.
Proline is an amino acid that contain
imino group (-NH) instead of amino
group (NH2)
39
40. Proline is the exceptional amino
acids which has a secondary amino
group called imino-group
In proline its propionyl side chain
forms an amide bond with its
primary amino group.
Hence proline is known as an
IMINO ACID
40
41. Naming amino acids
41
These 20 amino acids are given both three-letter and one-letter
abbreviations. Thus: alanine = Ala = A
42. Classification ofAmino acids
Based on R groups amino acids are classified as: (five)
Non-polar
Polar uncharged
Aromatic
Positively charged
Negatively charged
42
43. Non-polar (Hydrophobic) amino acids Further sub classifiedas:
A). Those that contain a non - polar aliphatic (linear hydrocarbon)
side chain. Includes:
43
44. B). Those that contain aromatic (cyclic or benzene ring and
derivative ring) side chain. Includes:
44
45. Polar (Hydrophilic)Amino acids Further classified as:
A. Positively charged (basic)
amino acids - contain an extra
amino group in their side
chain.
NB: For Histidine the one with
double bond is NH+ at
physiological pH when
histidine is incorporated in the
formation of polypeptides.
45
46. B. Negatively charged (acidic) amino acids - that contain an extra
carboxylic group in their side chain (in addition to the -carboxylic
group).
46
47. C. Uncharged amino acids -
contain no charged group in their
side chain.
Includes:
Serine and Threonine with
OH functional group
Cysteine with SH functional
group
Asparagine and Glutamine
with extra amino group.
47
48. The side chain of cysteine contains
a sulfhydryl group (–SH).
In proteins, the –SH groups of two
cysteines can become oxidized to
form a dimer, cystine, which
contains a covalent cross-link
called a disulfide bond (–S–S–)
through spontaneous (non-
enzymatic) oxidation of their
sulfhydryl groups
48
49. Arginine and Histidine are semi-essential. The healthy adult
human body synthesizes just enough arginine and histidine
but in:
the childhood growth period,
sickness,
convalescence (recovery) and
during pregnancy
such amount is not enough and requires dietary
supplementation and hence these amino acids become
essential. Therefore, these two amino acids are semi-essential.
49
50. Proteins
Proteins are polymers of amino acids. They are formed by linkage of
the constituent amino acids by a peptide bond.
Peptide bond is an amide bond formed by the covalent linkage of
(–OH) α-carboxyl group of one amino acid with the(-H) α-amino
group of another amino acid through condensation reaction (water
is released).
Requires an input of free energy
50
52. The series of three or more amino acids joined by peptide bonds is
referred to as a polypeptide chain.(more than 50 amino acids)
If two amino acids are joined together they form a dipeptide
where as if it is three amino acids, tripeptide.
A polypeptide chain has polarity (has a carboxyl or C- terminal
and a amino or N-terminal ends).
By convention, the amino end (N-terminal) is considered as the
beginning of a polypeptide chain.
52
53. Protein structure (orginzation)
Proteins are polypeptides with specific amino acid sequences.
Amino acid sequence determines the final three-dimensional
structure of a protein
Protein structure is generally described as having four levels
Primary
Secondary
Tertiary
Quaternary
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55. 1. Primary Structure
Is the sequence of amino acids in the polypeptide
It is formed by α-carboxyl of one amino acid + α -amino group of
another amino acid by the peptide bond.
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56. 2. Secondary Structure
Regular arrangement of amino acids within localized regions
Polypeptide chains fold Into regular periodic structures such as
The α helix (alpha helix) and
The β pleated sheet (beta pleated sheet)
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i) Alpha Helix : Is a spiral rod like
structure in which tightly packed
coiled polypeptide backbone with
the side chains extend outward in a
helical array to avoid interfering
sterically with each other
57. ii. Beta Sheets
Are almost fully extended
structures in which the
backbone of the polypeptide
chain is extended into a
zigzag/pleated form unlike
coiled -helix
The side chains extended out
ward in opposite directions.
Also known as β pleated
sheet b/c the surfaces appear
pleated
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58. 3. Tertiary structure
Is formed by folding of secondary structures into a large three-
dimensional organization that is mainly stabilized by non-covalent
interactions
It is the final three dimensional and functional structure of proteins.
The polypeptide chain folds so that its hydrophobic side chains are
buried and its polar, charged chains are on the surface.
Forces that stabilize protein structure
In addition to the peptide bond protein structure is stabilized by
different types of covalent and/or non-covalent bonds.
These are:
Disulfide bond
Hydrogen bond
Electrostatic interaction (Ionic bond or salt bridge) and
Hydrophobic interaction
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60. 4. Quaternary structure
Occurs in proteins that have multiple polypeptide chains, called
subunits.
The structure formed by monomer-monomer interaction in an
oligomeric protein is known as quaternary structure
Proteins with identical subunits are termed homooligomers but
those with d/t or distinct polypeptide chains are termed
heterooligomers
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61. Example: Quaternary structure (hemoglobin)
Hemoglobin is composed of
four polypeptide chains, each
of which is bound to a heme -
group.
The two α-chains and the two
β-chains are identical
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62. Denaturation of proteins
Protein denaturation is the unfolding and disorganization of the
secondary and tertiary structures of proteins due to breaking down
of the non covalent bonds that stabilize them.
There is no hydrolysis of the peptide bonds and hence the
primary structure is preserved.
Denaturing agents include:
Heat,
Organic solvents,
Mechanical mixing,
Strong acids or bases,
Detergents, and
Ions of heavy metals such as lead and mercury.
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63. Denaturation could be reversible, however most proteins, once
denatured, remain permanently disordered.
Hence denaturation is usually irreversible.
A cooked egg cannot be “uncooked”.
Denatured proteins are often insoluble and therefore precipitate
from solution.
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64. Classification of proteins
Proteins can be classified based on different criteria such as:
over all morphology (shape and size ).
function,
chemical composition,
biological or nutritional value.
A. Based on overall shape and size (Axial Ratio):
Based on their overall structure or shape proteins are generally
classified as:
Globular proteins and
Fibrous proteins.
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65. Globular proteins Fibrous proteins
Spherical in shape and
resemble irregular balls with
<10 axial ratio.
More liable to denaturation and
are easily soluble in water.
Most of the globular proteins
serve as enzymes, hormones,
transporters etc.
Examples are
immunoglobulins, albumin,
hemoglobin and insulin.
Shape usually is composed of
different secondary structures.
Have linear and elongated
structure with >10 axial ratio.
They are resistant to digestion
or denaturation and are
insoluble in water.
Hence majority of these proteins
have structural function.
Examples are keratin in hair,
skin and nail; elastin in lungs;
collagen in bones; and myosin
an tropomyosin of the muscles.
Shape is dominated by a single
type of secondary structure;
usually α-helix
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66. B). Based on nutritional (biological) value
Based on their nutritional value proteins can be classified as:
1. Complete (nutritionally rich) proteins - contain all the
essential amino acids.
Ex. casein of milk is a nutritionally rich protein.
2. Incomplete proteins - lack one essential amino acid for
example, cereal proteins lack lysine; and
3. Poor proteins - lack many essential amino acids. Ex, zein, a corn
protein lack tryptophan and lysine.
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67. C) Based on chemical composition
1) Simple proteins: contain only the amino acid residues.
Ex: Albumin, Globulins, protamines, histones, etc.
2) Compound or complex proteins: composed of a protein
and a non protein component (prosthetic group). The
protein component alone is called apoprotein.
The apoprotein combined with the prosthetic group is
called holoprotein.
Ex: Glycoproteins, lipoproteins, Heme proteins like
hemoglobin and myoglobin, Metaloproteins,
Nucleoproteins, Chromoproteins.
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68. Functions of proteins
Some of the primary functions of proteins are listed here.
Structural: Proteins are the main structural component in bone,
muscles, cytoskeleton and cell membrane.
Nutrition: Provide the body with essential amino acids,
nitrogen and sulfur. Some glucogenic amino acids can be
converted to glucose.
Catalytic: All metabolic enzymes are proteins in nature.
Endocrine: Most hormones and all receptors are protein in
nature.
Defense: The antibodies (immunoglobulins) and complement
system that play an important role in the body’s defensive
mechanisms are proteins in nature.
Osmotic Potential: Plasma proteins are responsible for most
effective osmotic pressure of the blood. This osmotic pressure
plays a central role in many processes, e.g., urine formation. 68
69. Blood clotting factors are proteins.
Transport role
Lipoproteins carry lipids in the blood forming lipoprotein
complexes (chylomicron, VLDL, LDL,HDL).
Proteins also carry, hormones, e.g., thyroid hormones and
minerals, e.g., calcium, iron and copper.
Hemoglobin carries O2 from the lung to tissues is a protein.
Membrane transport: The proteins in the membranes act as
channels or specific carrier proteins to allow selective
molecules/ions to cross into or out of the cells.
Gene expression: Most factors required for DNA replication,
transcription and mRNA translation are protein in nature.
Signal Transduction: Cell-environment, intercellular and
intracellular communication is carried out largely by proteins.
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