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BIOCHEMISTRY FOR 3RD YEAR BIOLOGY
MAJOR STUDENTS
By: Shiferaw A. (Ass’t. professor)
Course overview
Course title-Biochemistry
Course Code: Biol 3071
Credit hour=3, Or 5ECTS
Contact hour/wk=3 (2 theoretical classes + 1 practical/ week)
Evaluation:
Continuous assessment (50 %)
Chapter quiz = 15%
Test= 20%
Group assignment = 10%
Attendance and class participation = 5%
Final/End of semester Exam (50 %)
2
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
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
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
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
7
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
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
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
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
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
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
14
Prokaryotic Vs Eukaryotic cells
15
INTRODUCTION
1.3. Water and Chemical bonds in
Biochemistry
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
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
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
 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
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
 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
 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
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
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
26
 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
 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
INTRODUCTION
1.4. Biological buffer systems
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
 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
 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
 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
 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
 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
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
2. CHEMISTRY OF AMINO ACIDS
AND PROTEINS
2.1. Amino acids
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
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
 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
Naming amino acids
41
These 20 amino acids are given both three-letter and one-letter
abbreviations. Thus: alanine = Ala = A
Classification ofAmino acids
 Based on R groups amino acids are classified as: (five)
Non-polar
Polar uncharged
Aromatic
Positively charged
Negatively charged
42
Non-polar (Hydrophobic) amino acids Further sub classifiedas:
A). Those that contain a non - polar aliphatic (linear hydrocarbon)
side chain. Includes:
43
B). Those that contain aromatic (cyclic or benzene ring and
derivative ring) side chain. Includes:
44
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
B. Negatively charged (acidic) amino acids - that contain an extra
carboxylic group in their side chain (in addition to the -carboxylic
group).
46
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
 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
 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
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
51
 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
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
53
54
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.
55
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)
56
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
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
57
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
58
59
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
60
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
61
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.
62
 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.
63
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.
64
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
65
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.
66
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.
67
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
 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.
69

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1. intro,aa&amp; prot

  • 1. BIOCHEMISTRY FOR 3RD YEAR BIOLOGY MAJOR STUDENTS By: Shiferaw A. (Ass’t. professor)
  • 2. Course overview Course title-Biochemistry Course Code: Biol 3071 Credit hour=3, Or 5ECTS Contact hour/wk=3 (2 theoretical classes + 1 practical/ week) Evaluation: Continuous assessment (50 %) Chapter quiz = 15% Test= 20% Group assignment = 10% Attendance and class participation = 5% Final/End of semester Exam (50 %) 2
  • 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
  • 7. 7
  • 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
  • 14. 14
  • 16. INTRODUCTION 1.3. Water and Chemical bonds in Biochemistry
  • 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
  • 26. 26
  • 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
  • 37. 2. CHEMISTRY OF AMINO ACIDS AND PROTEINS 2.1. Amino acids
  • 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
  • 51. 51
  • 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 53
  • 54. 54
  • 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. 55
  • 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) 56 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 57
  • 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 58
  • 59. 59
  • 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 60
  • 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 61
  • 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. 62
  • 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. 63
  • 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. 64
  • 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 65
  • 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. 66
  • 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. 67
  • 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. 69