Biochemistry for Medical Laboratory Science 1
Base on the illustration there is a part of Hydrophilic
Chapter 1: Introduction
Hydrophilic are opposites of hydrophobic, they are water loving
molecules they don’t repel water.
Biochemistry
Because of the presence of hydrophilic and hydrophobic
Biological Chemistry
molecules on Palmitic Acid we can consider this molecule
Study of chemistry of the living organism. Includes
as an Amphipathic molecule which hydrophilic and
biomolecules, and biochemical reactions.
hydrophobic are both present.
Four Biomolecules of the body
1. Proteins Functional Groups
2. Carbohydrates - are group of atoms that renders the chemical properties of
3. ZxzLipids an organic molecules and biomolecules.
4. Nucleic Acids
Biomolecules-can be found in Plant and Animal cells
Cytological composition
1. 50-95 % water
2. 1% ions- magnesium, potassium, calcium ions
3. Other organic molecules
Organic Molecules
Are Carbon based molecules
Covalently bond to itself or other elements ex. H, O, N, S,
and P
Simplest organic
molecule
CH4 (methane)
Hydrocarbons
One of the most organic molecules
Are derived from Hydrogen and Carbons
If the hydrocarbons chains are longer the more it becomes
Non-polar and insoluble in water whether there is the
presence of OH.
Note that hydrocarbons are useless inside the body, the Note: Alcohol- OH group- Hydroxyl group
only thing that important in this compound is the
The presence of this group makes the biomolecules
derivative Hydrogen and Carbon.
abundant (can form hydrogen bonding) and polar.
Aldehyde- usually have smell (not that really good)
Hydrophobic and Hydrophilic
Acids- fatty acids are example of acids in lipids; some certain kind of
Hydrophobic are molecules that repels water that usually acids are found in acidic amino acids- bears the carboxyl group
are nonpolar molecules (makes a weak acid)
Example: Lipids/ fatty acids a monocarboxylic acid can be a
component of fat/oil. A good example of this is a Palmitic acid
Note: if H+ is easily remove it has a higher acidity; not all hydrogen
are acidic because it only becomes acidic when it is beside an
electronegative element.
Amines- a weak basic; had a positive charge when it accepts proton;
NH2 in amino acids.
“Whatever you decide to do, make sure it makes you happy.”
Paulo Coelho
, Biochemistry for Medical Laboratory Science 2
Thiol- contains Sulfur; important in the proteins which it forms the When we add a non-polar substance in water, water forms
disulfide bond. a cage around the non-polar substances. This situation is
Esters- makes up fat and acid. not favorable to water, because non-polar substances
Double bond is important in fatty acids; reactive site or serve interferes with the waters ability to interact with other
as like a dipole bond in fatty acids. water molecules.
1. Saturated- single bond When we add to or more non-polar substances to water,
2. Unsaturated- double bond the non-polar molecules will form together. This is
favorable because it releases the trapped water molecules
Chapter 2. Water: The Solvent for Biochemical Reactions and allows them to once more form hydrogen bonds with
other water molecules.
This interaction between non-polar molecules in water are
Polarity of Water called hydrophobic interactions and this effect is called
Water is not a linear molecule. hydrophobic effect.
Water molecule is bent thus, asymmetric distribution of
electron density occurs.
Oxygen of water has a high electronegativity which pulls
hydrogen electrons closer and creates a partial positive
charge.
Intramolecular Bonds and Intermolecular Bonds
Intramolecular Bonds – bonds that exist in any given molecules,
atoms interact with one another via these bonds.
1. Non-polar Covalent- formed between 2 two atoms by the
equal sharing of electrons. The electronegativity value of
the two atoms is equal.
Strong Intermolecular Bonds
2. Polar Covalent- unequal sharing of electrons that arises
By an electron forces water molecule can strongly interact due to different electronegativity values.
with each other. 3. Ionic Bond- one atom with so much more electronegativity
The partial positive charge part of hydrogen allows it to get pulls away the electron completely to its side from the
very close with other atoms oxygen atom. other atom.
This intermolecular bond is called a hydrogen bond.
Intermolecular Bonds – Bonds that exist between atoms of different
molecules. Considered as weaker than intermolecular bonds on a
one to one basis, there are usually many intermolecular bonds at
any given moment and this makes them a driving force in many
biochemical processes.
1. Hydrogen Bonds (dipole-dipole) - hydrogen atom is shared
by two electronegative atoms. Strongest intermolecular
bond; the group that has the H- atom is called the H-bond
donor, while the other group that accepts is the H-bond
acceptor.
2. London-Dispersion Forces (van der Waals) - the electron
density around atoms is not static but rather fluctuates
with the time. The asymmetric distribution of one
Hydrophobic Effect molecule can cause the electron density of a nearby
Because of the high polarity characteristic and to hydrogen molecules to change accordingly. The two molecules can
bond of water, it can easily dissolve other polar then bond through the instantaneous dipole moments.
substances.
In some situations, when we add sodium chloride in water, Acids and Bases
water can break the ionic bonds between Na and Cl, and Determines what the pH of a solution is.
form many other hydrogen bonds, this situation is pH is a factor that can influence the many different types
favorable. of biological processes that take place inside our body.
Non-polar molecules don’t interact favorably with water.
“Whatever you decide to do, make sure it makes you happy.”
Paulo Coelho
, Biochemistry for Medical Laboratory Science 3
pH can determine the final structure of a biological
molecules.
Acid and Base reaction
A hydrogen atom is exchanged between molecules.
One covalent bond is broken and one is formed.
Acid molecule donates H+ ion and a bond are broken
Base molecule accepts H+ ion because it has a lone pair of
electrons and it forms covalent bond.
𝑯𝑨 ↔ 𝑯+ + 𝑨− Acid dissociation
𝑯+ + 𝑯𝟐𝑶 ↔ 𝑯𝟐𝑶+𝑯 Base hydrogen in water exist
as hydronium molecules
The concentration of H ions is measured in terms of pH.
𝒑𝑯 = −𝒍𝒐𝒈[𝑯+]
A pH of 7.0 means that [H+] =1.0x10-7
𝟕. 𝟎 = −𝒍𝒐𝒈[𝑯+] → 𝟕. 𝟎 = 𝒍𝒐𝒈[𝑯+] → 𝟏𝟎−𝟕 = [𝑯+]
We can also use the pH to describe the concentration of
OH- in solution
𝑯𝟐𝑶 ↔ 𝑯+ + 𝑶𝑯− Amino Acid Structure and Properties
With the exception of glycine, all protein-derived amino
[𝑯+][𝑶𝑯−] acids have at least one stereo center (the a-carbon) and
𝑲=
[𝑯𝟐𝑶] are chiral (stereoisomers)
o the vast majority of a-amino acids have the L-
At room temperature, K=1.8x10-16 and the concentration configuration at the a-carbon (Proline is usually D)
of H2O in pure water is always equal to a constant value of Side-chain carbons in other amino acids designated with
55.5 Greek symbols, starting at a carbon (…etc)
[𝑯+][𝑶𝑯−]
𝟏. 𝟖𝒙𝟏𝟎−𝟏𝟔 = = 𝟏. 𝟎𝒙𝟏𝟎−𝟏𝟒 = [𝑯+][𝑶𝑯−] Amino acids can be referred to by three-letter or one-
𝟓𝟓. 𝟓 letter codes.
Therefore, at a pH=7, the concentration of hydroxide is
also 1.0x10-7 Individual Amino Acids
𝟏. 𝟎𝒙𝟏𝟎−𝟏𝟒 = (𝟏. 𝟎𝒙𝟏𝟎−𝟕)[𝑶𝑯−] → [𝑶𝑯−] = 𝟏. 𝟎𝒙𝟏𝟎−𝟕 Group A: Nonpolar Side Chains
1. Alanine – Ala – A
2. Valine – Val – V
3. Leucine – Leu – L
4. Isoleucine – Ile – I
5. Proline – Pro – P
6. Phenylalanine – Phe – F
7. Tryptophan – Trp – W
8. Methionine – Met – M
Chapter 3. Amino Acids and Peptides
Amino acids Features
Amino Acids Exist in a 3-D World Ala, Val, Leu, Ile, Pro contain aliphatic hydrocarbon group
Pro Pro has cyclic structure
Amino acid: a compound that contains both an amino group and a
carboxyl group Phe hydrocarbon aromatic ring
c-Amino acid has an amino group attached to the carbon Trp Indole ring side chain, aromatic
adjacent to the carboxyl group Met Sulfur atom in side chain
-carbon also bound to side chain group, R
R gives identity to amino acid Group B: Neutral Polar Side Chains
Two stereoisomers of amino acids are designated L- or D-. 1. Serine – Ser – S
Based on similarity to glyceraldehyde 2. Threonine – Thr – T
Important Structural Features: 3. Tyrosine – Tyr – Y
4. Cysteine – Cys – C
1. All 20 are a-amino acids
5. Glutamine – Gln – Q
2. For 19 of the 20, the a-amino group is primary; for proline,
6. Asparagine – Asn – N
it is secondary Amino acids Features
3. With the exception of glycine, the a-carbon of each is a
Ser, Thr Side chain is polar hydroxyl group
stereocenter
Tyr hydroxyl group bonded to aromatic
4. Isoleucine and threonine contain a second stereocenter
hydrocarbon group
5. 3, and 1-letter codes (ex. Glycine – Gly – G)
Cys Side chain contains thiol group (-SH)
Gln, Asn contain amide bonds in side chain
“Whatever you decide to do, make sure it makes you happy.”
Paulo Coelho
, Biochemistry for Medical Laboratory Science 4
Group C: Acidic Side Chains
1. Glutamic Acid – Glu – E
2. Aspartic Acids – Asp – D
Both have a carboxyl group in side chain
Can lose a proton, forming a carboxylate ion
These amino acids are negatively charged at neutral pH
Group D: Basic Side Chains
1. Histidine – His – H
2. Lysine – Lys – K
3. Arginine – Arg – R
Side chains are positively charged at pH 7
Amino acids Features
Arg side chain is a guanidino group
His side chain is an imidazole group Ionization of Amino Acids
Lys side chain NH3 group is attached to an aliphatic
Remember, amino acids without charged groups on side
hydrocarbon chain
chain exist in neutral solution as zwitterions with no net charge
Acidity: -COOH Groups
The average pKa of a α-carboxyl group is 2.19, which makes
them considerably stronger acids than acetic acid (pKa 4.76)
the greater acidity of the amino acid carboxyl group is due
to the electron-withdrawing inductive effect of the -NH 3+
group
Basicity
α-NH3+ groups: The average value of pKafor an a-NH 3+ group
is 9.47, compared with a value of 10.76 for a 2° alkylammonium ion
Guanidine Group Titration of Amino Acids
The side chain of arginine is a considerably stronger base When an amino acid is titrated, the titration curve
than an aliphatic amine represents the reaction of each functional group with the hydroxide
o basicity of the guanido group is attributed to the large ion
resonance stabilization of the protonated form
relative to the neutral form
Imidazole Group
The side chain imidazole group of histidine is a heterocyclic
aromatic amine
Uncommon Amino Acids
Each derived from a common amino acid by a modification:
hydroxylysine and hydroxyproline are found only in a
few connective tissues such as collagen
thyroxine is found only in the thyroid gland
Titration of Histidine with NaOH
“Whatever you decide to do, make sure it makes you happy.”
Paulo Coelho
Base on the illustration there is a part of Hydrophilic
Chapter 1: Introduction
Hydrophilic are opposites of hydrophobic, they are water loving
molecules they don’t repel water.
Biochemistry
Because of the presence of hydrophilic and hydrophobic
Biological Chemistry
molecules on Palmitic Acid we can consider this molecule
Study of chemistry of the living organism. Includes
as an Amphipathic molecule which hydrophilic and
biomolecules, and biochemical reactions.
hydrophobic are both present.
Four Biomolecules of the body
1. Proteins Functional Groups
2. Carbohydrates - are group of atoms that renders the chemical properties of
3. ZxzLipids an organic molecules and biomolecules.
4. Nucleic Acids
Biomolecules-can be found in Plant and Animal cells
Cytological composition
1. 50-95 % water
2. 1% ions- magnesium, potassium, calcium ions
3. Other organic molecules
Organic Molecules
Are Carbon based molecules
Covalently bond to itself or other elements ex. H, O, N, S,
and P
Simplest organic
molecule
CH4 (methane)
Hydrocarbons
One of the most organic molecules
Are derived from Hydrogen and Carbons
If the hydrocarbons chains are longer the more it becomes
Non-polar and insoluble in water whether there is the
presence of OH.
Note that hydrocarbons are useless inside the body, the Note: Alcohol- OH group- Hydroxyl group
only thing that important in this compound is the
The presence of this group makes the biomolecules
derivative Hydrogen and Carbon.
abundant (can form hydrogen bonding) and polar.
Aldehyde- usually have smell (not that really good)
Hydrophobic and Hydrophilic
Acids- fatty acids are example of acids in lipids; some certain kind of
Hydrophobic are molecules that repels water that usually acids are found in acidic amino acids- bears the carboxyl group
are nonpolar molecules (makes a weak acid)
Example: Lipids/ fatty acids a monocarboxylic acid can be a
component of fat/oil. A good example of this is a Palmitic acid
Note: if H+ is easily remove it has a higher acidity; not all hydrogen
are acidic because it only becomes acidic when it is beside an
electronegative element.
Amines- a weak basic; had a positive charge when it accepts proton;
NH2 in amino acids.
“Whatever you decide to do, make sure it makes you happy.”
Paulo Coelho
, Biochemistry for Medical Laboratory Science 2
Thiol- contains Sulfur; important in the proteins which it forms the When we add a non-polar substance in water, water forms
disulfide bond. a cage around the non-polar substances. This situation is
Esters- makes up fat and acid. not favorable to water, because non-polar substances
Double bond is important in fatty acids; reactive site or serve interferes with the waters ability to interact with other
as like a dipole bond in fatty acids. water molecules.
1. Saturated- single bond When we add to or more non-polar substances to water,
2. Unsaturated- double bond the non-polar molecules will form together. This is
favorable because it releases the trapped water molecules
Chapter 2. Water: The Solvent for Biochemical Reactions and allows them to once more form hydrogen bonds with
other water molecules.
This interaction between non-polar molecules in water are
Polarity of Water called hydrophobic interactions and this effect is called
Water is not a linear molecule. hydrophobic effect.
Water molecule is bent thus, asymmetric distribution of
electron density occurs.
Oxygen of water has a high electronegativity which pulls
hydrogen electrons closer and creates a partial positive
charge.
Intramolecular Bonds and Intermolecular Bonds
Intramolecular Bonds – bonds that exist in any given molecules,
atoms interact with one another via these bonds.
1. Non-polar Covalent- formed between 2 two atoms by the
equal sharing of electrons. The electronegativity value of
the two atoms is equal.
Strong Intermolecular Bonds
2. Polar Covalent- unequal sharing of electrons that arises
By an electron forces water molecule can strongly interact due to different electronegativity values.
with each other. 3. Ionic Bond- one atom with so much more electronegativity
The partial positive charge part of hydrogen allows it to get pulls away the electron completely to its side from the
very close with other atoms oxygen atom. other atom.
This intermolecular bond is called a hydrogen bond.
Intermolecular Bonds – Bonds that exist between atoms of different
molecules. Considered as weaker than intermolecular bonds on a
one to one basis, there are usually many intermolecular bonds at
any given moment and this makes them a driving force in many
biochemical processes.
1. Hydrogen Bonds (dipole-dipole) - hydrogen atom is shared
by two electronegative atoms. Strongest intermolecular
bond; the group that has the H- atom is called the H-bond
donor, while the other group that accepts is the H-bond
acceptor.
2. London-Dispersion Forces (van der Waals) - the electron
density around atoms is not static but rather fluctuates
with the time. The asymmetric distribution of one
Hydrophobic Effect molecule can cause the electron density of a nearby
Because of the high polarity characteristic and to hydrogen molecules to change accordingly. The two molecules can
bond of water, it can easily dissolve other polar then bond through the instantaneous dipole moments.
substances.
In some situations, when we add sodium chloride in water, Acids and Bases
water can break the ionic bonds between Na and Cl, and Determines what the pH of a solution is.
form many other hydrogen bonds, this situation is pH is a factor that can influence the many different types
favorable. of biological processes that take place inside our body.
Non-polar molecules don’t interact favorably with water.
“Whatever you decide to do, make sure it makes you happy.”
Paulo Coelho
, Biochemistry for Medical Laboratory Science 3
pH can determine the final structure of a biological
molecules.
Acid and Base reaction
A hydrogen atom is exchanged between molecules.
One covalent bond is broken and one is formed.
Acid molecule donates H+ ion and a bond are broken
Base molecule accepts H+ ion because it has a lone pair of
electrons and it forms covalent bond.
𝑯𝑨 ↔ 𝑯+ + 𝑨− Acid dissociation
𝑯+ + 𝑯𝟐𝑶 ↔ 𝑯𝟐𝑶+𝑯 Base hydrogen in water exist
as hydronium molecules
The concentration of H ions is measured in terms of pH.
𝒑𝑯 = −𝒍𝒐𝒈[𝑯+]
A pH of 7.0 means that [H+] =1.0x10-7
𝟕. 𝟎 = −𝒍𝒐𝒈[𝑯+] → 𝟕. 𝟎 = 𝒍𝒐𝒈[𝑯+] → 𝟏𝟎−𝟕 = [𝑯+]
We can also use the pH to describe the concentration of
OH- in solution
𝑯𝟐𝑶 ↔ 𝑯+ + 𝑶𝑯− Amino Acid Structure and Properties
With the exception of glycine, all protein-derived amino
[𝑯+][𝑶𝑯−] acids have at least one stereo center (the a-carbon) and
𝑲=
[𝑯𝟐𝑶] are chiral (stereoisomers)
o the vast majority of a-amino acids have the L-
At room temperature, K=1.8x10-16 and the concentration configuration at the a-carbon (Proline is usually D)
of H2O in pure water is always equal to a constant value of Side-chain carbons in other amino acids designated with
55.5 Greek symbols, starting at a carbon (…etc)
[𝑯+][𝑶𝑯−]
𝟏. 𝟖𝒙𝟏𝟎−𝟏𝟔 = = 𝟏. 𝟎𝒙𝟏𝟎−𝟏𝟒 = [𝑯+][𝑶𝑯−] Amino acids can be referred to by three-letter or one-
𝟓𝟓. 𝟓 letter codes.
Therefore, at a pH=7, the concentration of hydroxide is
also 1.0x10-7 Individual Amino Acids
𝟏. 𝟎𝒙𝟏𝟎−𝟏𝟒 = (𝟏. 𝟎𝒙𝟏𝟎−𝟕)[𝑶𝑯−] → [𝑶𝑯−] = 𝟏. 𝟎𝒙𝟏𝟎−𝟕 Group A: Nonpolar Side Chains
1. Alanine – Ala – A
2. Valine – Val – V
3. Leucine – Leu – L
4. Isoleucine – Ile – I
5. Proline – Pro – P
6. Phenylalanine – Phe – F
7. Tryptophan – Trp – W
8. Methionine – Met – M
Chapter 3. Amino Acids and Peptides
Amino acids Features
Amino Acids Exist in a 3-D World Ala, Val, Leu, Ile, Pro contain aliphatic hydrocarbon group
Pro Pro has cyclic structure
Amino acid: a compound that contains both an amino group and a
carboxyl group Phe hydrocarbon aromatic ring
c-Amino acid has an amino group attached to the carbon Trp Indole ring side chain, aromatic
adjacent to the carboxyl group Met Sulfur atom in side chain
-carbon also bound to side chain group, R
R gives identity to amino acid Group B: Neutral Polar Side Chains
Two stereoisomers of amino acids are designated L- or D-. 1. Serine – Ser – S
Based on similarity to glyceraldehyde 2. Threonine – Thr – T
Important Structural Features: 3. Tyrosine – Tyr – Y
4. Cysteine – Cys – C
1. All 20 are a-amino acids
5. Glutamine – Gln – Q
2. For 19 of the 20, the a-amino group is primary; for proline,
6. Asparagine – Asn – N
it is secondary Amino acids Features
3. With the exception of glycine, the a-carbon of each is a
Ser, Thr Side chain is polar hydroxyl group
stereocenter
Tyr hydroxyl group bonded to aromatic
4. Isoleucine and threonine contain a second stereocenter
hydrocarbon group
5. 3, and 1-letter codes (ex. Glycine – Gly – G)
Cys Side chain contains thiol group (-SH)
Gln, Asn contain amide bonds in side chain
“Whatever you decide to do, make sure it makes you happy.”
Paulo Coelho
, Biochemistry for Medical Laboratory Science 4
Group C: Acidic Side Chains
1. Glutamic Acid – Glu – E
2. Aspartic Acids – Asp – D
Both have a carboxyl group in side chain
Can lose a proton, forming a carboxylate ion
These amino acids are negatively charged at neutral pH
Group D: Basic Side Chains
1. Histidine – His – H
2. Lysine – Lys – K
3. Arginine – Arg – R
Side chains are positively charged at pH 7
Amino acids Features
Arg side chain is a guanidino group
His side chain is an imidazole group Ionization of Amino Acids
Lys side chain NH3 group is attached to an aliphatic
Remember, amino acids without charged groups on side
hydrocarbon chain
chain exist in neutral solution as zwitterions with no net charge
Acidity: -COOH Groups
The average pKa of a α-carboxyl group is 2.19, which makes
them considerably stronger acids than acetic acid (pKa 4.76)
the greater acidity of the amino acid carboxyl group is due
to the electron-withdrawing inductive effect of the -NH 3+
group
Basicity
α-NH3+ groups: The average value of pKafor an a-NH 3+ group
is 9.47, compared with a value of 10.76 for a 2° alkylammonium ion
Guanidine Group Titration of Amino Acids
The side chain of arginine is a considerably stronger base When an amino acid is titrated, the titration curve
than an aliphatic amine represents the reaction of each functional group with the hydroxide
o basicity of the guanido group is attributed to the large ion
resonance stabilization of the protonated form
relative to the neutral form
Imidazole Group
The side chain imidazole group of histidine is a heterocyclic
aromatic amine
Uncommon Amino Acids
Each derived from a common amino acid by a modification:
hydroxylysine and hydroxyproline are found only in a
few connective tissues such as collagen
thyroxine is found only in the thyroid gland
Titration of Histidine with NaOH
“Whatever you decide to do, make sure it makes you happy.”
Paulo Coelho
