BIOCHEMISTRY

Threonine Ethanol (-CH2CH3OH) Thr T

Sulfur-containing amino acids
Cysteine Sulfhydryl (-CH2SH) Cys C

IONIZATION
Methionine (-(CH2)2SCH3) Met M
Acidic amino acid
Aspartic acid Propanoic acid (-CH2CH2 COOH) Asp D
THE CELL Glutamic acid Ethanoic acid (-CH2COOH) Glu E
Amine of acidic amino acids
Asparagine Amide -CONH2 Asn N
CARBOHYDRATES Glutamine Amide -CH2CONH2 Gln Q
Ba s i c a m i n o a c i d s

AMINO ACID, PEPTIDES, Lysine

Arginine
Lys
Arg
K
R
PROTEINS Be n z e n e - c o n t a i n i n g a m i n o a c i d
Phenylalanine Phe F
Learning Objectives: Tyrosine Tyr Y
• At the end of the lesson, the learners should be able to: H e t e r oc y c l i c a m i n o a c i d s
Proline Pro P
• Classify standard amino acids based on side chain polarity.
Histidine His H
• Draw structures of standard amino acids.
Tryptophan Trp W
• Differentiate essential amino acids from non-essential
• Non-polar side ch ains (Hydrophobic) –
amino acids.
Gly, Ala, Val, Leu, Ile, Pro, Met, Phe, Trp
• Illustrate the acid-base properties of amino acids.
• Polar side chains (hydrophilic) – Ser, Thr,
• Show peptide bond formation and discuss the nature of
bond formed. Tyr, Cys, Gln, Asn, Asp, Glu, Lys, His, Arg
• Identify side-chain interactions. CLASSIFICATION ACCORDING TO HUMAN BODY
NOMENCLATURE OF AMINO ACIDS NEEDS
• Amino acids are building blocks of protein Essential amino acids – Amino acids that is not
• Consist of amino group (basic), Carboxyl group (acidic), synthesized in the body and are needed to be ingest
and an R group attached to a carbon atom from other.
•
PVT MAT HILL (TMRW FT HILK)
Non-essential amino acids – Amino acid that is
synthesize in the body.
An L-amino acid
• GASCDENQYPW

• Most are found in protein except α-amino acids Conditional amino acids – a type of non-

• α – amino group is attached to the α carbon atom essential Amino acid that are not essential, except in
• Glycine is optically inactive because of the 2 hydrogen times of illness and stress.
atoms attached to α carbon.
CLASSIFICATION ACCORDING TO SIDE CHAIN
Name R group Abrev POLARITY
Aliphatic or alkyl side-chain amino acids
• Non-polar Amino Acids – amino acid w/ a
Glycine -H Gly G
hydrophobic alkyl R group or aromatic rings.
Alanine Methyl (-CH3) Ala A
Valine Isopropyl (-CH2(CH3)2) Val V • Gly Ala Val Leu Ile Met Trp Phe Pro
Leucine Isobutyl (-CH2CH(CH3)2) Leu L • Polar neutral amino a cids – Amino acids w/
Isoleucine Sec.butyl(-CHCH3CH2CH3) Ile I an uncharged hydrophilic R group
Hydroxy -containing amino acids • Ser, Thr, & Tyr (-OH) Cys & Gln (extra uncharged -
Serine Methanol -CH2OH Ser S NH2), Asn (-SH)
• Positively charged polar a mino acids – THE CONFIGURATION OF AMINO
polar basic amino acids: Lys, Arg, His (a weak base)
ACIDS
• Negatively charged polar amino acids –
• L-amino acid – NH2 group is on the left of α
Polar acidic amino acids: Asp, Glu carbon.
Non-polar • Amino acids in proteins are L-configurated
Gly Their alkyl group contribute the non-polar • D-amino acid - NH2 group is on the right of α
Ala characteristic carbon.
Val • All amino acids except glycine have at least one
Leu asymmetric or chiral carbon atom, which makes them
Ile optically active
Met Metabolic precursor for cysteine • Proteins with both D-amino acid and L-amino acid do not
Trp Indole grp: both heterocyclic & aromatic fold properly →no proper catalysis
Phe Benzene (aromatic) ring
THE ACID-BASE PROPERTIES OF
Pro Found at the beginning of protein or side of
helices w/c allows proteins to twist
AMINO ACIDS
• Amino acid can be an acid or a base depending on the pH
Polar neutral
in which they are dissolved in.
Ser Presence of OH group makes them polar;
• Because of this property, amino acids can be used as
Thr can H-bond buffers.
Tyr
Cys The only AA that forms disulfide bridges; Amphoteric property of amino acids
has sulfhydryl Amino group can be protonated → Basic portion

Gln Amide group are polar; can H-bond Carboxyl group can be deprotonated → Acidic portion

Asn • Zwitterion – a compound that has a negative

Positively charged polar (Basic) charge on one atom and a positive charge on a
Lys Additional Amino group nonadjacent atom
Arg Has guanidine; Amino group • Amino acids are Zwitterions that exists as a dipolar ion
His Has imidazole, the heterocyclic ring on its • Go back to this section for the pKa
side chain with an amino attached
A vasodilator
Cause swelling during allergy
Negativ ely charged polar (A cidic)
Asp Extra carboxyl group makes them polar; pH= 0 → Both groups are protonated → positively charged
Glu can H-bond pH= 7 → Carboxyl group deprotonates, and amino group
• Basic amino acids are positively charged because the protonates → neutral charge, except other acidic or basic AA

net charge of 2 protonated amino groups (-NH3+) and pH= 12 → Both groups are deprotonated → negatively charged

deprotonated carboxyl group (-COO-) is positive. • Amino acids can never exist as an uncharged compound,
• Acidic amino acids are positively charged because the regardless of the pH of the solution
net charge of 1 protonated amino group (-NH3+) and 2
deprotonated carboxyl groups (-COO-) is negative. ISOELECTRIC POINT
• Isoelectric point (pI) – of an acid is the pH at
which it has no net charge.
• It is the pH at which the amount of positive charge and
negative charge on an amino acid are balanced
 pI= pH at which there is no net charge • + charged amino acids → - electrode
• - charged amino acids → + electrode
• At pI, almost all amino acids in a solution are in its
• Amino acid in its zwitterion form does not migrate.
zwitterion form

If the pH value < pI of an amino acid → anionic PEPTIDE BOND FORMATION

If the pH value > pI of an amino acid → cationic
• Peptide bond – The amide bond between the free amino
group (-NH3+) of an amino acid and the free carboxylic
If the pH value = pI of an amino acid → zwitterion form
group (-COO-) of another amino acid
CALCULATING ISOELECTRIC POINT W/O AN • Link amino acids
IONIZABLE SIDE CHAIN

CALCULATING ISOELECTRIC POINT W/ AN IONIZABLE

SIDE CHAIN
• In the given example, the ionized side chain is an pKa
value of 10.79 (a value that can be obtained from the table
below)

• In naming attached amino acid or peptide, suffix “-yl” are

used for all the amino acid except the C-terminal amino
acid
• Each amino acid in the peptide chain has the L
configuration unless otherwise specified.
i.e: Valinylcysteinylalanine is tripeptide chain where the
blue is the N-terminal amino acid, and the red is the C-
terminal amino acid

AMINO ACID INTER & INTRA

MOLECULAR BONDS
NOTE: Amino acid chains could either have
interactions with other amino acid chains or it could
happen within a single amino acid chain

HYDROPHOBIC INTERACTION
• Non-polar R-groups of amino acids form intermolecular
hydrophobic bonds
• Gly Ala Val Leu Ile Met Trp Phe Pro

ION INTERACTION
SEPARATING AMINO ACIDS • Exhibited by deprotonated acidic amino acid and
protonated basic amino acid
(ELECTROPHORESIS) • Also called salt bridge
• Method used to separate amino acids in an electrical
• Interaction between Arg, Lys, & His (basic) and Glu & LEVELS OF PROTEIN STRUCTURES
Asp (acidic)
• The positive portion of basic amino acid interacts with the PRIMARY STRUCTURE
negative portion of the acidic amino acid. • Structure that determined by the sequence of amino acid
peptide chains.
HYDROGEN BONDING • A single alteration on the amino acid chain can change the
• Intermolecular bond between -OH, -SH, -NH containing function, make it less functional, or nonfunctional
amino acid • Disulfide bridges hold different portions in the protein
• Formed from electronegative atoms with electropositive together.
hydrogen
• Usually polar neutral molecules SECONDARY STRUCTURE
• Ser, Thr, & Tyr (-OH) Cys & Gln (extra uncharged - • Folding and bending of the polypeptide chain due to
NH2), Asn (-SH) intramolecular hydrogen bonds
• Intramolecular hydrogen bond maintains the shape of the
DISULFIDE BOND protein.
• Disulfide Bridge - Bond formed two cysteine
bonded together by mild oxidation
ALPHA-HELIX
• Spiral structure consisting of a tightly packed polypeptide
• Disulfide - A Strong covalent bond formed when
backbone.
two S are mildly oxidized together to form a S–S bond. • Intrachain hydrogen bonds stabilizes the folded helical
• Bond strength of disulfide (chemical bond) > hydrogen backbone
bond (intermolecular bond). • Each turn of the helix contains 4 amino acid residues.
• Found between nonadjacent amino acids in peptides and • Side chains of the α-carbons faces outwards of the helix
proteins. to minimize steric strain.
• Contribute to the overall shape of protein. • Each H amide nitrogen hydrogen bond with carboxyl O
• Interchain disulfide bridges – disulfide of an amino acids 4 amino acids away.
bridges between two different polypeptide chain. • Each turn contains 3.6 amino acids.
• Intrachain disulfide bridges – Disulfide • The repeat distance of the helix is 5.4 angstrom
bridges within a polypeptide chain. • Not all amino acids are capable of forming α helix due to
their R group causing steric crowding or could not fit
STACKING INTERACTION OR PI-PI COMPLEXATION into the helix properly.
• weak attractive, non-covalent interaction between • Two adjacent amino acids with like charges could not also
aromatic rings it due to repulsion.
• Phe, Trp, Tyr • L-amino acid chain →right-handed helix
• D-amino acid chain → left-handed helix
STRUCTURE OF PROTEINS • Forms fibrous and stretchable proteins (Keratin,
• A large molecule composed of amino acid chains bonded
collagen, elastic)
by peptide bonds that process biological processes
• Proteios (Greek) – holding first place. ΒETA-PLEATED SHEETS
• An amino acid • A polypeptide backbone zigzag structure.
• Peptides: fewer than 50 amino acids • Stabilized by interchain hydrogen bonds with neighboring
• Dipeptides: 2 amino acids peptide chains.
• Tripeptides: 3 amino acids • R groups that are between the chains must fit well in the
• Polypeptides : more than 10 amino acids center to maximize the hydrogen-bonding interaction
• Proteins: more than 50 amino acids between the two intra chains.
• 100 to 10,000 amino acid chains
• CHON
• Average of 2 amino acid repeat distance is 7.0 angstrom.
• Forms not stretchable proteins. (Enzymes, peptide
hormones, hemoglobin )

TERTIARY STRUCTURE
• 3D structure of the entire protein
• Hydro phobic interactions between nonpolar R
• Large-scale folding of the secondary structures within the
groups
protein and with the immediate environment.
• Helices and pleated sheets interact, arrange, and • Hydrogen bonding between nearby amino
organized relative to each other. acids
• Proteins fold spontaneously in solution to maximize their • Ionic bond between positive R groups with
stability; folds in a way that maximizes the number of negative R groups
stabilizing interactions. • Disulfide bridges
• Polar (hydrophilic) portions remain unfolded;
faces outer surface of the protein→ maximize contact QUATERNARY STRUCTURE
with water. • Describes the way the subunits are arrange and interact
• Non-polar (hydrophobic) regions tend to with one another
fold into a globular shape; faces inwards towards other • Subunits – Individual chains of proteins
nonpolar amino acids → minimizes contact with water.
• Monomer – a single protein subunit
• Domain – This shape is determined by the tertiary
• Dimer – one with two subunits
structure that contains folded sequence of 100 – 200
• Trimer – one with three subunits
amino acids within a protein.
• Hemoglobin – a tetramer that is part of the blood that
The domain structure dictates the protein function contains Fe stores O.
Changes in the primary and secondary structure that • Subunits are held by the same interactions that tertiary
affect the shape of the domain can change protein structures have.
function
TYPES OF PROTEINS
• Fibrous protein s – relatively rigid proteins and
often play structural roles. PROTEINS ACCORDING TO COMPOSITION
• Globular proteins – flexible proteins and play SIMPLE PROTEINS
regulatory roles. • Gives only α - amino acids when hydrolyzed.
1. albumin - in egg
2. globulins – myosin in muscle
3. glutelin – glutenin in wheat & oryzenin in rice
4. Prolamins – zein in corn, gliadin in wheat, hordein in
barley
5. Albuminoids – elastin in tendons, keratin in hair,
fibrosin in silk
 CONJUGATED PROTEINS Organic Solvents or Detergents – denatures
• Simple proteins linked with non-protein groups proteins on the nonpolar groups of the protein; disrupts
hydrophobic interaction.
1. Chromoprotein – proteins linked w/ a colored
compound. Heat or agitation – increase in molecular motion
Example: hemoglobin in blood disrupts the attractive forces

2. Glycoproteins – proteins linked w/a Renaturation – reverse process of denaturation

carbohydrate.
COAGULATION
Example: mucin in saliva
• Process of clumping small molecules together and form
3. Phosphoprotein – protein linked w/ H3PO4. aggregates
Example: casein in milk; vitellin in egg yolk • Changes the liquid state of the molecule
4. Nucleoproteins – proteins linked w/ nucleic • Coagulated protein tends to precipitate.
acids.
Example: nuclei in nuclei of cells NUTRITIONAL CONNECTION
5. Lipoproteins – proteins linked w/ fatty acid.

PROTEIN ACCORDING TO NUTRITIVE VALUE

Complete or adequate proteins – contains
essential al amino acids
Incomplete or inadequate proteins – lacks
one or more of the essential amino acids
PROTEINS ACCORDING TO FUNCTION
1. Catalytic action – enzymes
2. Regulatory – hormones such as insulin
3. Antibody proteins – for defense against
foreign bodies
4. Transport – hemoglobin; serum albumin
5. Buffer – hemoglobin
6. Structural – collagen in tendons, keratin in skin,
hair, nails, wool, horn & feathers; elastin in arteries
& skin
7. Blood coagulant – fibrin
8. Germicidal – anti-tumor-peptide antibiotic such
as Gramicidin A

PROTEIN DENATURATION
• Denaturation – is the change in shape caused by
the breaking of bonds that maintain the 3d shape of
the protein

FACTORS CAUSING DENATURATION

pH level – changes the charges on many side chains;
disrupts electrostatic attractions and H bonds.

Denaturing reagents – forming stronger H bonds to

protein groups that are stronger than the H bonds between the
protein structures. (Urea and guanidine hydrochloride)