1.

02
23, June, 2015 Dr. Phylis Rio | Amino Acids, Peptides, Protein Structures
LEARNING OBJECTIVES
 An amino group (-NH2)
Amino Acids:  A "variable" group or "R" group (side chain)
1. To describe the basic structure of amino acids
2. To discuss the classifications and basis for
classification of amino acid
3. To discuss the different properties of amino acids
4. To discuss the different reactions involving amino
acids
5. To discuss the special of functions of amino acids
6. To give the special groups in the different amino
acids

Protein and Structures:

1. To define protein
2. To give the functions of proteins Proline
3. To describe the formation of peptide bond  R with three-carbon chain that joins the nitrogen
4. To describe the characteristics of peptide bond to the alpha-carbon in a five-membered ring-
5. To differentiate configuration and conformation IMINO ACID
6. To describe the different protein structures or
order of organization
7. To discuss the different bonds involved the
different protein structures
8. To discuss the process of protein folding
9. To discuss other complex proteins
10. To explain clinical disorders involving proteins

AMINO ACIDS AMINO ACID CLASSIFICATION

 Building block of proteins I. BASED ON STRUCTURE

 300 naturally occurring-20 common A. Aliphatic
 Short polymers= Peptides
 Mono amino mono carboxylic acids
 Can contain D or L α-amino acids
1. simple – glycine, alanine
 Most are L α-amino acids; D amino-
microorganisms 2. branched chain – valine, leucine,
 All amino acids follow levorotatory (L- isoleucine
configuration of L-glyceraldehyde) 3. hydroxylic - serine, threonine
4. sulfur containing – cysteine, methionine
*Most amino acids are alpha amino acids (except 5. amino acid with carboxamide group-
proline- imino acid) – means amino group is attached to asparagine, glutamine
same carbon atom to which carboxyl group is attached
 Mono amino dicarboxylic ( acidic) – aspartic
Selenocysteine acid (aspartate), glutamic acid (glutamate)
 -L α-amino acids in peroxidises and reductases-  Diamino monocarboxylic (basic) – lysine,
catalysis of electron transport reactions arginine, histidine
 -Se atom replaces Sulfur of its structural analog,
cysteine
 -not spec. With a 3-letter codon

AMINO ACID STRUCTURE

 A carbon (the alpha carbon)

 A hydrogen atom (H)
 A carboxyl group (-COOH)

Transcribers: De Los Reyes, Fernandez, Flores, Guevarra, Javier, Lanuza, Libit, Maaño, Molina, Pagatpatan Page 1 of 13
1.02 BIOCHEMISTRY
Dr. Phylis Rio | Amino Acids, Peptides, Protein Structures

SULFUR-CONTAINING AMINO ACIDS

SIMPLE AMINO ACIDS

AMINO ACIDS with CARBOXYAMIDE GROUPS-

MONO AMINO DICARBOXYLIC (ACIDIC)

BRANCHED AMINO ACIDS

AMINO ACIDS with CARBOXAMIDE GROUPS-

DIAMINO MONOCARBOXYLIC (BASIC)
HYDROXY AMINO ACIDS

Transcribers: De Los Reyes, Fernandez, Flores, Guevarra, Javier, Lanuza, Libit, Maaño, Molina, Pagatpatan Page 2 of 13
1.02 BIOCHEMISTRY
Dr. Phylis Rio | Amino Acids, Peptides, Protein Structures

A. Amino acids with nonpolar side chains

 electrons are equally shared between carbon
and hydrogen atoms in side chains, so cannot
form hydrogen bond
 hydrophobic in nature
 Amino acids:
1. Alanine
B. Aromatic amino acid 2. Valine
-histidine (His [H]) 3. Leucine
-phenylalanine (Phe [F]) 4. Isoleucine
-tyrosine (Tyr [Y]) 5. Methionine
-tryptophan (Trp [W]) 6. Proline
7. Phenylalanine
8. Tryptophan
9. Glycine

B. Amino acids with uncharged or non-ionic polar side

chain

 hydrophilic in nature
 Amino acids:
1. Serine
2. Threonine
3. Tyrosine
4. Cysteine
5. Glutamine
C. Imino acid 6. Asparagine
-proline (Pro [P])
-not an alpha amino acid  amide group in Asparagine and Glutamine and
Hydroxyl group in Serine, Tyrosine and
Threonine can form hydrogen bond
 Sulfur in Cysteine can form disulfide bond
leading to formation of Cystine

C. Amino acids with charged or ionic polar side chain

 Acidic amino acids – with negative charge in the

R group; Aspartic acid, Glutamic acid
Special Groups in Side Chains of Amino Acids  Basic amino acids – with positive charge in the
1. arginine – guanidinium R group; Lysine, Arginine, Histidine
2. phenylalanine – benzene
3. tyrosine – phenol  Hydrophobic Amino Acids – Alanine, Isoleucine,
4. tryptophan – indole Leucine, Methionine, Phenylalanine, Proline,
5. histidine – imidazole Tryptophan, Valine, Glycine
6. proline – pyrrolidine  Hydrophilic – Arginine, Asparagine, Aspartic
acid, Cysteine, Glutamic acid, Glutamine,
II. BASED ON SIDE CHAIN CHARACTERS Histidine, Lysine, Serine, Threonine, Tyrosine
 Hydrophobic amino acids are found in the
*hydrophobic vs hydrophilic interior of proteins and hydrophilic amino acids
 properties that affect their location in a protein’s are found in the exterior
mature folded conformation

Transcribers: De Los Reyes, Fernandez, Flores, Guevarra, Javier, Lanuza, Libit, Maaño, Molina, Pagatpatan Page 3 of 13
1.02 BIOCHEMISTRY
Dr. Phylis Rio | Amino Acids, Peptides, Protein Structures

Derived Amino Acids

A. Found in protein – Additional amino acids that arise

III. BASED ON METABOLIC FATE
*amino acids are the main building blocks for protein
synthesis; in certain situations, however, amino acids
can be metabolized to compounds that can either form
glucose (glucogenic) or ketone bodies (ketogenic)
by the post-translational modification of an amino acid
already present in a peptide e.g. hydroxyproline.
B. Not seen in protein – e.g. ornithine & citrulline, which
are metabolites in urea biosynthesis
C. Non-alpha amino acids– no α-carbon present in the
structure e.g. gamma amino butyric acid (GABA) derived
from glutamic acid; β-alanine, β-aminoisobutyrate
PROPERTIES OF AMINO ACIDS

A. Purely ketogenic – L  all have high melting point

 can enter metabolic pathway of lipid; gives rise  all are soluble in water and alcohol (polar solvent)
to acetyl CoA but insoluble in nonpolar solvent (benzene)

ACID-BASE PROPERTY

 Amphoteric/Ampholytes
 the α-COOH and α-NH2 groups in amino acids
are capable of ionizing (as the R-groups of the
acidic and basic amino acids)
 charged and uncharged forms of the ionizable –
COOH and –NH3+ in protonic equilibrium:




B. Ketogenic and glucogenic –W, I, F, Y, K*

 carbon skeleton can enter ketogenic and
glucogenic pathways
 *Lysine is considered in some references as
purely ketogenic
C. Purely glucogenic – other 14 amino acids
 Yields pyruvate, or four- and five-carbon
 amino group – has lone pair of electron which can
intermediates of the citric acid cycle
impact the BASIC characteristics (-NH2)
IV. BASED ON NUTRITIONAL REQUIREMENT  carboxyl group – possess acidic hydrogen as a
result of pi electric delocalization that stabilizes
A. Essential Amino acids – M, I, L, K, V, F, T, W the tricentric molecular orbital that involves –
COOH
 Their carbon skeleton cannot be
synthesized by human and are  ionization state of an amino acid varies with pH
preformed and are taken in food  in acidic solution, they are cationic in form
B. Semi-Essential – H, R  the amino group is protonated (NH3+) and
 not essential in adult but essential for carboxyl group is not dissociated (COOH)
proper growth in children
 important in preterm infant in whom a
developmental delay in specific enzymes involved
in amino acid synthesis have been demonstrated
C. Non-essential - remaining 10 amino acids

Transcribers: De Los Reyes, Fernandez, Flores, Guevarra, Javier, Lanuza, Libit, Maaño, Molina, Pagatpatan Page 4 of 13
1.02 BIOCHEMISTRY
Dr. Phylis Rio | Amino Acids, Peptides, Protein Structures

 in alkaline solution, they behave as anions

 the carboxyl group GIVES its proton

 At physiological pH (7.4), carboxyl group is

upronated and amino group is pronated.
 if amino acid has no ionizable R group 
it is electrically neutral at 7.4 pH and in
dipolar form
 When an amino acid is dissolved in water, it
exists in solution as the dipolar ion/zwitterion
(German for “hybrid ion”)
 Zwitterion/ampholyte – can be acidic or
basic in nature
 molecular species that bear no
net charge ( + charge = - charge)
 acid – proton donor

 base – proton acceptor

Transcribers: De Los Reyes, Fernandez, Flores, Guevarra, Javier, Lanuza, Libit, Maaño, Molina, Pagatpatan Page 5 of 13
1.02 BIOCHEMISTRY
Dr. Phylis Rio | Amino Acids, Peptides, Protein Structures

 As organic acids, the acidic strength of the  Important information about titration curves:
carboxyl, amino and ionizable R groups in amino 1. quantitative measure of the pKa of each of
acids can be defined by association constant Ks the ionizing groups
or commonly the negative logarithm of Ka or pKa 2. number of regions of buffering power
(lower pKa value = stronger acid  can easily (depending on the number of flat portions in
dissociate ion) the curve)
 pKa – acid strength of weak acids 3. relationship between the amino acid’s net
 strong acids = low pKa value electric charge and pH
weak acids = high pKa value  any amino acid has a net negative
 high Ka  high acidity charge at any pH above its pI (acidic)
 pKa  negative logarithm of Ka ( - log  move toward the positive
Ka) electrode (anode) when placed in an
 low pKa = highly acidic electric field
 net charge (algebraic sum of all the charges in  at any pH below its pI, any amino
groups present) of an amino acid depends upon acid will have a net positive charge
the pH of the medium (basic)  move toward the negative
 as the pH changes, so do the charges as electrode (cathode)
observed in titration  the FARTHER THE pH from its
 when net charge of an amino acid is zero, the pH isoelectric point, the greater the net
will be equivalent to an isoelectric point electric charge of the amino acid’s
molecules
ISOELECTRIC POINT (pI)
OPTICAL PROPERTY
 the pH at which amino acid will carry no charge
 all the groups are ionized but charges cancel  Chiral – structurally asymmetrical molecule
each other  Amino acids are chiral the tetrahedral Carbon
 no mobility in an electric field with four different substituent
 solubility and buffering capacity will be minimum  Glycine is not chiral since its R group is H,
therefore it is not optically active
Additional Information Regarding Titration  Chirality – describes handedness of a molecule
(Acc. to Lehninger – as discussed by Dr. Rio but not
present in slides)  Ability to rotate the plane of polarized light to
 acid-base titration – gradual addition or removal either to the right (dextrorotatory, D) or to the left
of protons (levorotatory, L)
 amino acids have characteristic titration  All amino acids are in L configuration
curves unique to them  D-amino acids are never found in protein; they
 example: titration curve of glycine (how to exist in nature as synthetic compounds like
interpret and read) antibiotics.

 at very low pH, the predominant ionic species of
glycine is the fully protonated form (+H3N – CH2 –
COOH)
 midpoint of the first titration  point of
inflection where pH is equal to the pKa of
the protonated group being titrated
 another point of inflection  removal of the first
proton is essentially complete and the removal of
the second has just begun
 glycine exists as the dipolar ion: +H3N –
CH2 – COO- ***because of the presence of asymmetric carbon atom;
 second stage of titration: removal of a proton from mirror images are formed with reference to the alpha-
the –NH3+ group of glycine carbon atom and are called D and L isomers
 pH is equal to the pKa for the NH3+ group

 Aromatic AA, such as tryptophan (W),

 titration is essentially complete at a pH of 12  tyrosine (Y), phenylalanine (F), and histidine
predominant form of glycine is H2N – CH2 – COO-

Transcribers: De Los Reyes, Fernandez, Flores, Guevarra, Javier, Lanuza, Libit, Maaño, Molina, Pagatpatan Page 6 of 13
1.02 BIOCHEMISTRY
Dr. Phylis Rio | Amino Acids, Peptides, Protein Structures

(H), can absorb UV light with a maximum  Involves the hydroxyl group
absorbance in the range of 280nm.  The hydroxyl group of hydroxyl amino acids (serine,
threonine, and tyrosine) can form an esters with
 Ability of protein to absorb UV light is due to phosphoric acid to form phosphoproteins
the presence of predominant tryptophan.
3. Reaction of Amino Group
CHEMICAL REACTIONS  Side chains containing another amino group other
than a-amino group such as those found in
 Based on the different molecules found in the glutamine and asparagine can form n-glycosidic
structure of the protein, it can undergo different bonds with carbohydrates to form glycoproteins.
chemical reactions:
4. Reacton with sulfahydryl (-SH) group
I. REACTIONS DUE TO CARBOXYL GROUP  Amino acids containing sulfur (cysteine,
methionine) can bond with another cysteine to form
1. Decarboxylation - removal of the carboxyl group. a disulfide bond.
-produce important amine
Histidine -> histamine and carbon dioxide
Tyrosine -> tyramine and carbon dioxide SPECIAL FUNCTIONS OF AMINO ACIDS

2. Amide formation - the carboxyl group of the dicarboxylic 1. GABA from glutamic acid and dopamine from tyrosine –
amino acid, other than the alpha carbon, can combine with neurotransmitters
the ammonium to form the corresponding substances or 2. Histamine – mediator of allergic reactions
molecules: 3. Thyroxine – thyroid hormone
4. Histidine - buffering activity, found in reactive center of
Aspartic acid + ammonia = asparagine enzymes, can donate and accept electrons
Glutamic acid + ammonia = glutamine 5. Lysine - binding of coenzymes like pyridoxal phosphate
and biotin
II. REACTIONS INVOLVING AMINO GROUP 6. Ornithine and citrulline derived from arginine –essential
in urea synthesis
1. Transamination
 Alpha amino group is transferred to a-ketoacid to PROTEINS
form a new amino acid and a-ketoacid
 Glutamic acid + pyruvate a-ketoglutarate + alanine  Polymerization of amino acids to form the structural
framework of proteins
2. Oxidative deamination  Peptide bond formation is the most important
 Alpha amino group is removed from amino acid reaction of amino acids
to form the corresponding ketoacid and
ammonia. Peptides are used as:
 Glutamic acid is the most common and 1. Hormones (e.g. insulin)
important amino acid that undergoes this 2. Neurotransmitters (e.g GABA)
reaction 3. Antibiotics (e.g. Gramicidin A)
4. Regulators (e.g. Glutathione)
3. Formation of Carbamino compounds 5. Anti-tumor agent (e.g. Bleomycin)
 occurs at alkaline pH and serves as a
mechanism for the removal of CO2from the By convention, N-terminal end is written at the left while the
tissues and lungs by hemoglobin C-terminal end is written at the right
 Carbon dioxide + amino group -> carbamino
group Peptide Bond
 formed when alpha carboxyl group of one amino
III. REACTIONS DUE TO SIDE CHAIN acid reacts and condenses ( non enzymatically )
with alpha amino group of another amino acid with
1. Trans-methylation loss of water
 Methyl group of methionine after activation is  CO – NH bridge
transferred to an acceptor which becomes  also called amide bond
methylated and forms a homocysteine
 Methionine + methyl group -> homocysteine

2. Ester formation by OH group

Transcribers: De Los Reyes, Fernandez, Flores, Guevarra, Javier, Lanuza, Libit, Maaño, Molina, Pagatpatan Page 7 of 13
1.02 BIOCHEMISTRY
Dr. Phylis Rio | Amino Acids, Peptides, Protein Structures

 rigid and planar (O, C, N, and H atoms of a peptide

bond are coplanar)
 trans in nature (except Proline)
 side chains are free to rotate on either side of
peptide bond

# of peptide bonds = # of AA residues minus one, e.g. a 3

amino acid residue (a tripeptide) will form 2 peptide bonds

 Some contain unusual amino acids: in mammals,

peptide hormones typically contain only the α-
amino acids of protein linked by a peptide bond.
Other peptides, however, contain non-protein
amino acids, derivatives of amino acids, or amino
acids linked by an atypical peptide bond.

Protein / Related System Function

Enzyme Catalytic
Hemoglobin O2 transport, buffer
Defense against foreign
Antibody
bodies
Hormone Regulatory
Collagen, Keratin, Elastin Structural
Actin and Myosin Contraction
Peptides are Polyelectrolytes
HOW TO DRAW A PEPTIDE BOND  The peptide bond is uncharged at any pH of
physiologic interest.
1. Use a zigzag to represent the main chain or backbone  Formation of peptide is accompanied by a net
(HN-CH-C=O). By convention, peptides are written with loss of one positive and one negative charge per
the residue that bears the free α- amino group at the left. peptide bond formed.
2. Add the main chain atoms: α-nitrogen, α-carbon, o Peptides are charged molecules at
carbonyl carbon. physiologic pH owing to their COOH and
3. Add a hydrogen atom to each α-carbon and to each NH3 terminal groups, and, where
peptide nitrogen, and an oxygen to the carbonyl carbon. present, their acidic or basic R groups.
4. Add the appropriate R groups to each α-carbon atom.
5. Three-letter abbreviations linked by straight lines Peptide Bond has Partial Double-Bond Character
represent an unambiguous primary structure. Lines are  Peptides are written as if a single bond linked to
omitted for single-letter abbreviations the α- COOH and α-NH3 atoms, this bond
e.g. Asp-Ala-Ser exhibits partial double-bond character.
 There is no freedom of rotation about the bond
that connects the carboxyl carbon and the
CHARACTERISTICS OF PEPTIDE BOND nitrogen of a peptide bond.
 partial double bond; no freedom of rotation

Transcribers: De Los Reyes, Fernandez, Flores, Guevarra, Javier, Lanuza, Libit, Maaño, Molina, Pagatpatan Page 8 of 13
1.02 BIOCHEMISTRY
Dr. Phylis Rio | Amino Acids, Peptides, Protein Structures

 The imposed semirigidity of peptide  When sequence is changed, polypeptide is also

bonds has important consequences for higher changed
orders of protein structure.

Non-covalent Forces Constrain Peptide Conformation

 Folding of a peptide probably occurs coincident
with its biosynthesis.
 The physiological conformation reflects the
collective contributions of the amino acid
sequence, steric hindrance, and non-covalent
interactions between residues.  Primary Structure Determines Biologic Activity
 Peptides and proteins with specific  A single amino acid change ( mutation )
conformations in a linear sequence may have profound
effect on the function
 Example in normal hemoglobin ( Hb A);
STRUCTURES OF PROTEINS amino acid in the beta chain – glutamic
acid but in sickle cell anemia it is
Configuration
changed to valine
 Geometric relationship between a given set of
atoms
 L- and D-amino acids or L- and D-isomers Regular Conformations in Protein
Two broad classes
Conformation 1. Globular – compactly folded and coiled
 Spatial relationship of every atom in a molecule 2. Fibrous – more filamentous or elongated
 3-D arrangement
 Inter-conversion between conformers that
occurs between covalent bonds without rupture
SECONDARY STRUCTURE
Rotation about a single bond  Protein or portions of protein exhibit regularly
 Proteins have different levels of structural repeating types of structures
organization: Primary, Secondary, Tertiary and  Two common regular conformations – alpha helix
Quaternary and beta pleated sheet
 In that folding, it occurred that the amino acids  Stabilized by hydrogen bond, formed
are of the opposite charge; hence they attract between the carbonyl group one amino acid
each other and form ionic bonds. But if they had to amide group of another amino acid
like charges, they will repel.
 Proteins have different levels of structural
organization: primary, secondary, tertiary and
quaternary.
PRIMARY STRUCTURE

 Denotes the number and sequence of amino

acids in protein.
 Polymerization of amino acids – polypeptide
chain
 Each amino acids in the chain is called residue
 Structure is linear and linkage is maintained by
peptide bond
 Higher levels of organization are decided by
primary structure
 Each polypeptide chain has a unique amino acid
sequence decided by the gene sequence as
encoded in the genetic code
 Gene codes not only determine the order of
amino acids in a protein, but they also determine
a protein's structure and function
ALPHA HELIX
 It is the common structure of globular class
 Polypeptide chain is twisted to form coil spiral
 Tightly coiled peptide backbone forms the inner part
and side chains extend outward
 Stabilized by intrachain of hydrogen bond
 Carbonyl carbon ( CO )of one amino acid forms H
bond with amine hydrogen (NH) of another amino
acid that is situated four residues further down the
chain

Transcribers: De Los Reyes, Fernandez, Flores, Guevarra, Javier, Lanuza, Libit, Maaño, Molina, Pagatpatan Page 9 of 13
1.02 BIOCHEMISTRY
Dr. Phylis Rio | Amino Acids, Peptides, Protein Structures

NON REGULAR SECONDARY STRUCTURES

- Include bends and loops that reside on the
surface of proteins and constitute accessible
sites (epitopes) for recognition and binding of
antibodies

Short segments of
amino acids that join
two units of secondary
 Essentially all alpha helices are right handed structure; such as two
Turns and Bends
adjacent strands of an
 Amino acids that favor alpha helix formation –
antiparallel sheet (ie.
alanine, aspartic acid, glutamic acid, leucine,
proline and glycine are
isoleucine, methionine
present in β turns).
 Disrupts helix (produces bend) – glycine, proline
Regions that contain
 Example of structures with alpha helix – keratin,
residues beyond the
collagen, fibrin
minimum number
Loops
necessary to connect
adjacent regions of
secondary structure.

SUPER SECONDARY STRUCTURES (Motif)

 Formed by combination of secondary structure
BETA PLEATED SHEET elements (alpha helices, beta sheets, nonregular
sequences)
 Amino acid residues form a zig-zag or pleated
pattern in which R groups of adjacent residues  Considered as a structural motif intermediate
point in opposite directions. between secondary and tertiary structures
 Composed of stretches of at least 5 – 10 amino  I.e. helix loop helix motif
acids called beta strands.
 Peptide backbone is highly extended.
TERTIARY STRUCTURE
 Derives much of its stability from hydrogen
bonds between the carbonyl oxygens and amide
 Refers to the complete 3D structure of
hydrogens of peptide bonds.
polypeptide units of a given protein.
 Denotes how the secondary features assemble
Two Types of β -pleated sheet
to form domains and how these domains relate
adjacent peptide chains proceed
spatially to one another.
in the same direction ( the
o Domain - section of a protein structure
direction of N terminal to C
sufficient to perform a particular
terminal end is the same)
Parallel chemical or physical task such as
binding of a substrate or other ligand.
 Accurate 3D structure-folding is assisted by a
chaperone inside the cell.
 Incorrect folding may produce an alteration in
adjacent chains are aligned in protein structure (Prion Disease).
Antiparallel opposite directions (ie. – fatty acid
binding protein)

Transcribers: De Los Reyes, Fernandez, Flores, Guevarra, Javier, Lanuza, Libit, Maaño, Molina, Pagatpatan Page 10 of 13
1.02 BIOCHEMISTRY
Dr. Phylis Rio | Amino Acids, Peptides, Protein Structures

refers to the interaction of

Charge-Dipole ionized R groups with dipole
water
interaction of R groups of
Dipole-Dipole
amino acids

3. Van der Waals Forces

 These are weak forces of attraction
between polar and nonpolar molecules
therefore molecules should be nearer.
 These forces are the summation of
various forms of energy resulting from
momentary random fluctuation in the
distribution of electrons around any
atom which give rise to a transient
unequal distribution of electron or an
electric dipole.
4. Disulfide bond
Examples of Tertiary Structure Proteins (Murray, 2009)
 Covalent bonding between the "R"
groups of cysteine amino acids.
Important features of the Tertiary Structure:
QUATERNARY STRUCTURE
1. Interior formed by amino acids with hydrophobic
side chains / R groups.
2. Surface formed largely of hydrophilic amino acids  multiple polypeptide chains assembled into
that interact with aqueous environment. oligomeric proteins
 The stabilizing forces that hold the polypeptide
BONDS FORMING THE TERTIARY STRUCTURE: subunits together are the same forces that are
responsible for tertiary structure stabilization
 Interaction between R groups of the amino acids  describes the arrangement and position of each
would favor formation of additional hydrogen of the subunits in a multiunit protein.
bond, hydrophobic bond, ionic/ electrostatic
bonds, Van der Waals forces and disulfide “A major force stabilizing the quaternary structure is the
bridge. hydrophobic interaction among nonpolar side chains at
the contact regions of the subunits. Additional stabilizing
1. Hydrophobic Bonds forces include interactions between side chains of the
 These are formed by the interaction subunits, including electrostatic interactions between
between nonpolar hydrophobic side ionic groups of opposite charge: hydrogen bonds
chains. between polar groups; and disulfide bonds”
 Bonds cause nonpolar molecules to
adhere to another.
2. Electrostatic / Ionic Bonds
 These are attractive forces between two
opposite charges or repulsion between
two like charges.

Types of Charges
refers to attraction between
Charge-Charge oppositely-charged amino
acids 2 TYPES
Homo-oligomers – with identical subunits
Hetero-oligomers – with several distinct subunits

Transcribers: De Los Reyes, Fernandez, Flores, Guevarra, Javier, Lanuza, Libit, Maaño, Molina, Pagatpatan Page 11 of 13
1.02 BIOCHEMISTRY
Dr. Phylis Rio | Amino Acids, Peptides, Protein Structures

Ex. Hemoglobin – with 2 alpha and 2

beta subunits.

Protein Folding
 Folding is modular and considered as dynamic
process
 Occurs via stepwise process

1st stage: short segments of newly synthesized

polypeptide fold into secondary structural units
2nd stage: hydrophobic regions aggregate into interior of
the protein forming a “molten globule”

 Molten globule - a partially folded polypeptide in

which modules of secondary structure rearrange
until mature conformation is attained.

 Each element of secondary or supersecondary

structure facilitates proper folding by directing
the folding process toward the native
conformation and away from unproductive
alternatives

 Proteins that assist in folding: protein disulfide

isomerase, proline-cis, trans - isomerase and
chaperones

Chaperones
 binds to short sequences of hydrophobic
amino acids in newly synthesize
polypeptides, shielding from solvent
 prevent aggregation
 provide opportunity for formation of
appropriate secondary elements and
formation of molten globules

COMPLEX PROTEINS

1. Glycoproteins CLINICAL SIGNIFICANCE

 covalently conjugated
 present in the surface of RBC, used in Collagen - most abundant structural protein
blood typing Alterations of collagen due to abnormal genes or
2. Lipoproteins abnormal processing results in following disorders:
 associated with lipids which aid in 1.Ehlers- Danlos Syndrome
storage and transport of other lipids. Ex. 2. Osteogenic imperfecta
HDL and LDL 3. Marfan’s Syndrome

Familial Hypercholesterolemia - due to genetic defect in

gene encoding the receptor for LDL

Carcinogenesis – basic structure of protein is disrupted

by mutation in their genes

Transcribers: De Los Reyes, Fernandez, Flores, Guevarra, Javier, Lanuza, Libit, Maaño, Molina, Pagatpatan Page 12 of 13
1.02 BIOCHEMISTRY
Dr. Phylis Rio | Amino Acids, Peptides, Protein Structures

5. What is the product of the arachnoid acid that

aids in blood coagulation?
 Thromboxanes
6. What are the processes that are needed to
make a short amino acid longer?
 Elongation
CASE DISCUSSION 1 QUIZ  Desaturation
7. What is the precursor of the EPA?
 α-linolenic acid (ALA)
1. What are the two ends of a fatty acid?
8. What is the pathway that you should inhibit in
 Methyl
order to stop arthritis?
 Carboxyl
 Cyclooxygenase pathway (pro-
2. What are the three main Polyunsaturated Fatty
inflammatory pathway)
Acids (PUFA)?
9. Since we already have ω-6 FAs in our body, we
 α-linolenic acid (ALA)
don’t need to include ω-3 FA in our diet or
 Eicosapentaenoic acid (EPA) supplements. True or false?
 Docosohexenoic acid (DHA)  False. ω-3 FAs are essential FAs since
3. If a cell membrane is full of unsaturated fatty they cannot be synthesized by our
acids, it becomes rigid. True or false? bodies and therefore should be taken up
 False. Unsaturated FAs contain double in our diet.
bonds therefore creating “kinks” on their 10. What is the enzyme that aids ω-6 FAs to
end. This makes the cell membrane become ω-3 FAs?
more fluid as compared to saturated  None. This is a trick question since,
FAs that create a rigid CM because of again, ω-3 FAs cannot be synthesized
the absence of double bonds/kinks on by our bodies and can only be obtained
their tails. through eating food rich in ω-3 (salmon,
tuna etc.) or taking in supplements (fish
oil).

4. Differentiate the 3 PUFAs from #2 in terms of

bonds.

(Number of carbons in
chain):(number of double bonds)n--
(position of last double bond from
methyl end)

Transcribers: De Los Reyes, Fernandez, Flores, Guevarra, Javier, Lanuza, Libit, Maaño, Molina, Pagatpatan Page 13 of 13