BIOCHEMISTRY LECTURE

8/17/2022 ● Unicellular - Yeasts and Paramecium

THE UNIT OF BIOLOGICAL ORGANIZATION: THE CELL
● All living creatures are composed of cells.
● Most cells are similar in size.
● Multicellular - Animals and Plants
● Existence of organelles is the difference between
prokaryotic and eukaryotic cells.
● Organelle: Membrane-enclosed portion of a cell with a
specific function.

A COMPARISON OF PROKARYOTES AND EUKARYOTES

Organelle Prokaryotes Eukaryotes

Nucleus No definite Present

nucleus; DNA
present but not
separate from the
rest of the cell.

Cell membrane Present Present

THE CLASSES OF CELLS (plasma
1. Bacteria membrane)
2. Archaea
3. Eukaryote Mitochondria None; enzymes Present
for oxidation
● Before, the cells were studied based on qualitative data. reactions located
on plasma
● There are only two major types of cells:
membrane
○ Prokaryotes
○ Eukaryotes Endoplasmic None Present
● When it is already possible to characterize the living reticulum
system molecularly, they saw a lineage that thrives in
harsh environments (Archaea). Ribosomes Present Present
○ Archaea are similar to bacteria, but they are
not the same. Chloroplasts None; Present in green
photosynthesis (if plants
○ They came from the same origin (Phylogeny
present) is
studies) localized in
chromatophores
Based on morphology:
● The two great classes of organisms have different cell
Mitochondria
types.
● Where oxidative phosphorylation happens where ATP
● Prokaryotic cells are uncompartmentalized;
is generated. The enzymes for oxidative
○ Uncompartmentalized - there are no
phosphorylation are present in the plasma membrane.
rooms. They coexist with one another.
● Eukaryotic cells are compartmentalized due to the
ANIMAL, PLANT VS PROKARYOTIC CELL
presence of membrane bound organelles.
○ Organelle - structure that is surrounded by
its own membrane and performs a specific
function.

PROKARYOTES AND EUKARYOTES

Prokaryotes
● Microorganisms that lack a distinct nucleus and
membrane-enclosed organelles.
● Include bacteria and cyanobacteria.
● They still have their own DNA, it is concentrated in a
region called nucleoid.
● Includes bacteria and cyanobacteria.

Eukaryotes
● Organisms whose cells have a well-defined nucleus
and membrane-enclosed organelles.
 BIOCHEMISTRY LECTURE
Which of the three can you readily identify to distinguish it
with the others?
Answer: Prokaryotic Cell, they do not have well defined
organelles.
How to distinguish a Plant from an Animal cell?
Answer:
● The presence of the chloroplast (sagot ni paul),
● Presence of the big vacuole present in the plant cell.
Why does the plant cell have a big vacuole compared to
the animal cell?
Answer: To maintain water balance (Frances), FOR
STORAGE (food) (bat kailangan magstore ng plant, ano main
difference nila in physical qualities? > mobility
Animals can look for its food & since plants are immobile
it has to store its nutrients
What is the block/black structure in the endoplasmic
reticulum?
Answer: Ribosomes (bilog bilog)
● In the nucleus there is a region that is dark -
Nucleolus
● The DNA replicate is used for the RNA transcription .
● RNA serves as a template for protein synthesis.
● Ribosomes are the site of protein synthesis.
● When the RNA is transcribed, the RNA transcript is
exported through the nuclear pore so that it reaches
its destination, that is the Ribosome which is the site
of synthesis.
The Ribosomes are either stranded on the endoplasmic
reticulum or cytoplasm/cytosol, now which ribosome
would be the destination of the RNA transcript? Saan sila
pupunta?
● Depende kasi the protein after translation or while
translated can be modified, ang tawag when
modification is post translational processes. Now
these processes are happening in the endoplasmic
reticulum and continue in the golgi apparatus.
● So saan papunta yung RNA transcript would be
dependent on if it would be modified after
translation or not modified.
● If:
○ NOT MODIFIED - sa cytosol
○ MODIFIED - it has to go through the
different channels of the endoplasmic
reticulum and to the golgi apparatus.
Post Translational Processes - happen in the endoplasmic
reticulum and continue in the golgi apparatus.
CELL WALL
The plant and the prokaryotic cell have a cell wall, but the
composition of the two cell walls is different.
The material of the plant cell wall (made of)?
● Cellulose
Bacterial cell wall?
● Peptidoglycan, conjugate of peptide and
carbohydrate
TYPICAL PROKARYOTE
Schematic view of a representative bacterial cell.
● The DNA molecule that constitutes most of the genetic
material is coiled up in a region called the nucleoid, which
shares the fluid interior of the cell (the cytoplasm) with
ribosomes (which synthesize proteins), other particles,
and a large variety of dissolved molecules.
● The cell is bounded by a plasma membrane, outside of
which is usually a fairly rigid cell wall (made up of
cellulose).
● Many bacteria also have a gelatinous outer capsule
(Distinction between gram positive and gram negative).
● Projecting from the surface may be pili (responsible for
cell attachment), which attach the cell to other cells or
surfaces, and one or more flagellae, which enable the cell
to swim through a liquid environment.
● Concentrated in the region called nucleloid.
● Even though walang nucleus ang prokaryotes, meron pa
rin silang DNA concentrated lang sa isang region na
nucleoid.
EUKARYOTIC CELLS
● Includes multicellular organisms such as plants and
animals, protist and fungi.
● Have subcellular organelles.
● Three of the most important organelles are the:
○ nucleus,
○ mitochondrion and
○ chloroplast.
 BIOCHEMISTRY LECTURE
TYPICAL ANIMAL CELL CHLOROPLASTS

● Are the site of photosynthesis in plants and other

photosynthesizing organisms.
● Are bounded by two membranes enclosing a fluid-filled
What is the difference between the Smooth and Rough stroma that contains enzymes.
endoplasmic reticulum? ○ The membrane is a bilayer.
○ Stroma - The space enclosed by the two
Answer: The rough endoplasmic reticulum has the presence membranes.
of ribosomes. ● Membranes inside the stroma are organized into
thylakoids that house chlorophyll.
TYPICAL PLANT CELL ● Chlorophyll absorbs solar energy and carbohydrates are
made in the stroma.
● Do not be confused that the membrane is a bilayer
enclosing. So that there is a fluid called stroma enclosed
by the two membranes.
● Thylakoids house the chlorophyll.

MITOCHONDRIA

What is the difference between a plant cell and an animal

cell?

Answer: May peroxisome, chloroplast & cell wall yung plant

cell compared sa animal cell.

NUCLEUS

● Mitochondria is surrounded by an outer and an inner

membrane, and in between the two is called the inter
membrane space.
● The Inner membrane has several infoldings, called
cristae.
○ The infoldings increase surface area per
volume.
● The inner membrane is the one that houses the proteins
of electron transport chain & ATP synthase which
releases the ATP from the complex once synthesized.
● This is where the DNA is kept and RNA is transcribed.
● The electron transport chain (ETC) is the one responsible
RNA is transported out of the nucleus through the nuclear
for oxidative phosphorylation which ends with the
pores. Proteins needed inside the nucleus are transported
synthesis of ATP.
in through the nuclear pores.
● The ETC and the ATP are embedded in the inner
● The nucleolus is usually visible as a dark spot in the
membrane.
nucleus and is the site of ribosome formation
 BIOCHEMISTRY LECTURE
Kaya if maraming infoldings, magiging advantageous ba to in
terms of ATP production?
Answer: Yes!
The ETC is responsible for oxidative phosphorylations.
ETC is a chain.
ATP is embedded in the membrane.
Cristae increases the surface area. That would lead to a
higher amount of ATP.
The space that is surrounded by the inner membrane is called
the matrix.
MITOCHONDRIA
● Are the sites of aerobic respiration, and generally are
the major energy production center in eukaryotes.
● Are found in plant and animal cells.
● Are bounded by a double membrane surrounding
fluid-filled matrix.
● The inner membranes of mitochondria are cristae.
● The matrix contains enzymes that break down
carbohydrates and the cristae house protein
complexes that produce ATP.
● Have their own DNA and their own ribosomes; and
those ribosomes are more similar to bacterial
ribosomes than to eukaryotic ribosomes.
- It is where ATP is generated.
If they have their own DNA, are the mitochondrial DNA
different to nuclear DNA.
Answer: Yes ,The maternal ancestry can be traced through
the mitochondrial DNA.
In fact, yung process of replication medyo magkaiba yung
nuclear DNA pati mitochondrial DNA.
THE ENDOPLASMIC RETICULUM
● The endoplasmic reticulum (ER) is a system of
membranous channels and saccules.
● The ER is the transport network for molecules targeted for
certain modifications and specific final destinations, as
opposed to molecules that are destined to float freely in
the cytoplasm.
● Rough ER is studded with ribosomes and is the site of
protein synthesis and processing.
● Smooth ER lacks ribosomes and is the site of synthesis of
phospholipids and the packaging of proteins into
vesicles, among other functions.
THE GOLGI APPARATUS
● The Golgi apparatus consists of a stack of curved
saccules.
● The Golgi apparatus receives protein and also lipid-filled
vesicles from the ER, packages, processes, and
distributes them within the cell.
● This organelle may also be involved in secretion.
LYSOSOMES AND VACUOLES
Contains enzymes
● Lysosomes are vesicles produced by the Golgi apparatus.
● Lysosomes contain hydrolytic enzymes and are involved in
intracellular digestion.
● Vacuoles (large) and vesicles (small) are membranous
sacs in the cell that store substances.
- Enzymes that hydrolyzes a macromolecule or
compound and are present in intracellular digestion.
If a protein is engulfed by a lysosome, what would happen to
the protein? It would be digested to what?
Answer: It becomes amino acids (hydrolized)
Terms > Vacuole (big), vesicle (small)
PEROXISOMES
Contains enzymes
● Peroxisomes are vesicles that contain catalase
(enzymes).
● This enzyme degrades hydrogen peroxide to water and
oxygen.
- Proxisome; lysosol
- Lysosol ung enzyme
- H202 - reactive oxygen species
● H2O2 is one of the reactive oxygen species. The final
oxygen acceptor of oxygenated phosphorylation is
oxygen and it is reduced to water. Incomplete oxidation
of oxygen leads to the reactive oxygen species and one
of them is H2O2.
Imagine if the cell contains large amounts of H2O2, will it be
destructive for the cell? Yes kasi reactive sya kaya
dinedegrade ng peroxisome to water.
Catalase can dismutate hydrogen peroxide to water and
oxygen.
Answer: Is it disastrous? It has something that countereffect
that molecule.
RIBOSOMES
●
● Protein Synthesis occurs at tiny organelles called
ribosomes.
● Ribosomes are composed of a large subunit and a small
subunit.
● Ribosomes can be found alone in the cytoplasm, in groups
called polyribosomes, or attached to the endoplasmic
reticulum.
- Two subunits: Large and Small
CYTOSOL
● It is the liquid inside the cell.
● Viscous liquid; it contains dissolved metabolites.
○ Contains a lot of enzymes.
● Has internal organization
 BIOCHEMISTRY LECTURE
● Has fine strands that holds the organelles in place (called
microtrabecular lattice or cytoskeleton)
- Enzyme
- It is not a homogenous liquid but it has internal
organization. Pag wala yun the organelles present
inside the cell would be moving around.
Viscous kasi it contains dissolved metabolized enzymes
Without internal organization, the organelles present inside the
cell are still moving around. Cytoskeleton holds the
organelles in place. Parang mga tali raw lamaw
○ That pathway converts lipids back to
carbohydrates.
○ Glyoxylic acid is the formed intermediate.
Name 2 other organelles that contain enzymes that catalyze
the glyoxylate cycle/pathway (meaning it contains several
reactions) eme:
1. Lysosomes
2. Peroxisomes (Contain enzymes)

THE CYTOSKELETON
● The eukaryotic cytoskeleton is a network of filaments and
tubules that extends from the nucleus to the plasma
membrane.
● The cytoskeleton contains three types of elements
responsible for cell shape, movement within the cell,
and movement of the cell:
1. Microtubules (diameter: 22μm, e.g. Tubulin)
2. Microfilaments (diameter: 6 μm, e.g. Actin
filaments)
3. Intermediate filaments (diameter: 7-11μm)

- Shape, movement Within and of the cell CELL FRACTIONATION

- There are 3 types and they are based by their Fractionation - broken into different organelles.
diameter. ● In order for a cell to be fractionated, the sample containing
- Smallest is microfilaments the cell needs to be homogenized.
● The cell membrane has to be broken so that all the
THE MICROTRABECULAR LATTICE organelles are released into the medium.

Homogenization Fractional Centrifugation

● Grinding in a mortar ● A technique used to

and pestle and an separate cellular
abrasive substance like components.
sand. ● Done after
● Sonicator - Breaking homogenization.
the cell under high
pressure.
● Using an electric
homogenizer consisting
● The organelles seen here are the endoplasmic reticulum, of a teflon pestle in a
glass tube.
the mitochondria and the ribosome.
● These organelles are placed in position because of the ● After Homogenization, ginagawa ung fractional
presence of the cytoskeleton. Centrifugation.

Yung mga tali tali yung cytoskeleton - Fractionation - broken into different organelles.

GLYOXYSOMES What can you understand from fractionation?

● Are formed only in the plant cells
● Not present in animal cells.
● Contain enzymes that catalyze the glyoxylate cycle, a
pathway that converts lipids to carbohydrates with
glyoxylic acid as an intermediates.
○ Composed of several reactions and each
reaction is catalyzed by a specific enzyme.
What is broken apart in the cell? Or the cell is broken into
what?
- into different organelles. In order to fractionate it into
different organelles, it has to be homogenized.
- SECOND BULLET - SONICATOR tawag sakanya??
 BIOCHEMISTRY LECTURE
Which would be the first to precipitate or settle when
centrifugation is done?
Answer: The heaviest
- G is another unit of revolution instead of RPM this is
quite slow
- Only the heaviest organelles would precipitate
(Nucleus and other cell debris with the same weight)
- Supernatant is transferred to another tube increasing
to another revolution
- After 5 mins the mitochondria pero and lyso would
settle
- Transfer supernatant again to another tube and
increase speed again
- The lightest would settle
Then transfer again the supernatant to another tube increasing
the speed and the lightest would settle. THe supernatant will
contain the dissolved materials, enzyme, and molecules.
If you need mo cytosol lang, how would you design the
fractionation?
1. Prepare the homogenate
2. Centrifuge na agad to 100,000 g kasi cytosol lang
naman ang kailangan.
If mitochondria lang, yan na yung step by step para matanggal
yung unneeded components.
AMINO ACIDS AND PEPTIDES
● Proteins are cells’ workhorses as it performs several
functions in the cell.
● There are 20 standard amino acids. God is a painter
○ Amino acids - serves as a palette of colors.
PEPTIDE
● Materials made up of amino acids but the # is less than 50
amino acids.
● Peptide and protein are made up of link amino acids but
differ in size.
○ Peptides are shorter than proteins
PROTEINS AND PEPTIDES
● Proteins can be distinguished by the number, composition,
and sequence of amino acid residues.
Example:
Tripeptide
1. Alanine - Glycine - Methionine
2. Methionine - Glycine - Alanine
3. Glycine - Alanine - Methionine
Although the composition is the same, how do they differ
Answer: Differ in terms of sequence/order. Peptides and
proteins are both made up of link amino acid polymers but
differ in size.
● Linked Amino acid polymers of 50 or less are peptides;
polymers greater than 50 are proteins or polypeptides.
● There are 20 standard amino acids.
TOTAL NUMBER OF AMINO ACIDS: 22 (may nadagdag na
dalawa)
Definition of Standard Amino Acids
● These are the amino acids that are genetically encoded
which means that they are coded or have specific codons
in the genetic code.
● Take note that the genetic code has 64 codes.
● Three of the 64 codes are for stop codons.
● The remaining 61 codes are for the 20 amino acids.
● These 2 recently discovered amino acids use one of the
three stop codons.
 BIOCHEMISTRY LECTURE
PROTEIN DIVERSITY
● Depending on the amino acid composition of the protein,
the protein or peptide would fold into its native
conformation.
● We can classify proteins in terms of structure into
globular or fibrous proteins.
○ Globular - bilog
○ Fibrous - stick (collagen in picture)
● A lot of protein has more than one polypeptide chain.
Example:
Catalase and Hemoglobin -
❖ Have more than 1 polypeptide chain/subunits.
❖ Each polypeptide chain would constitute one
subunit.
● The net interactions of the polypeptide chains would give
rise to its native conformation.
● The native conformation / final structure of the protein
in nature would dictate the function of the protein.
● Some of these functions would require globular protein.
AMINO ACIDS - THE BUILDING BLOCKS OF PROTEINS
● The 20 standard amino acids share a common structure
but differ in their side chains.
● Peptides and Proteins are amino acid polymers.
○ These amino acids are linked together by
peptide bonds.
● Peptide bonds link amino acid residues in a polypeptide.
● Some amino acid side chains contain ionizable groups
whose pK values may vary.
GENERAL STRUCTURE OF THE ɑ-AMINO ACIDS
Based on the figure:
● Ɑ Carbon - Left most connected to a carboxyl group
(RCOH)
● R group - side chain / residue (tira or iwan)
Reason why it is called as Residue:
● An amide/peptide is formed when a carboxyl and an
“amino” group react to form an peptide bond. (dipeptide)
● In a protein or peptide polymerization, the carboxylate of
the amino acid would react with the amino group of the
second amino acid to form an amide bond (type of
peptide bond).
○ Result: Dipeptide
● The second amino acid has s a free carboxylate that can
react with another amino acid through the amino group
with the third.
When the peptide bond is formed, what is left in the amino
acid that is still seen in the polymer? (unchanged?)
Answer: R group
It is the residue that would give character to the whole
protein/peptide.
If single amino acid:
● It is still the residue that gives the amino acid character.
● Amino acids are classified based on the side chain.
3 MAJOR CLASSIFICATIONS OF AMINO ACIDS
GROUP A. NON-POLAR or POLAR
NON-POLAR
● The amino acid is non-polar.
● The side ch ain is composed of hydrocarbons (C-H)
(aliphatic or aromatic)
POLAR
● The presence of an electronegative atom (Oxygen O
or Nitrogen N)
GROUP B. Polar Side chains that are uncharged at
physiological conditions
● The amino group is positively charged and the
carboxyl group is negatively charged.
Form of amino acid at physiological conditions at 7.4
● The carboxylate is a carboxylate at pH lower than 7.4,
the proton is ionized already.
○ The pK values of the Ɑ-Carboxylate is
around ≈ 2 (or below). Definitely at pH 7.4 it
is already ionized. deprotonated
○ The Ɑ-Amino group, the usual pK values
range from around 8-10. Therefore at pH 7.4
it is protonated.
● Therefore, the net charge of the figure is uncharged.
PROTONATED + DEPROTONATED = UNCHARGED
 BIOCHEMISTRY LECTURE
GROUP C. Polar side chains that are charged at Meaning of Each Category
physiological conditions ● Residue Mass (D)b
Random Notes: ● Average Occurrence in Proteins (%)c - how frequent are
The amino group is positively charge they found in proteins.
Carboxylate is negatively charged ● pK1 Ɑ-COOHd - The pK value of the alpha carboxylic acid.
It is #3 at 7.4 the pKa is lower than 7.4 (MGA BANDANG 2) ● pK2 Ɑ-NH3+d - The pK value of the alpha amino group.
At 7.4 it is protonated ● pKR (for the side chains)
The figure is the protonated form.
TO BE FURNISHED ● Non-Polar amino acids do not have an ionizable group
in their side chains.
INDIVIDUAL AMINO ACIDS: THEIR STRUCTURES AND
PROPERTIES ALANINE
GROUP A. AMINO ACIDS WITH NONPOLAR SIDE CHAINS

● R group: Methyl Group

VALINE

Ala = Alanine Pro = Proline

Val =Valine Phe = Phenylalanine

● R group: Isopropyl Group
Leu = Leucine Trp = Tryptophan
LEUCINE
Ile = Isoleucine Met = Methionine
Total: 8
Sa book: 9 , walang Glycine ● R group: Isobutyl Group
● They are represented by a one letter entry symbol. The
composition and order must be specified. Which is why ISOLEUCINE
they devised 3 letter symbols.
● The three letter symbol is usually the first three letters of
the amino acid.
● The one letter symbol is usually the first letter of the amino ● R group: Secbutyl Group
acid written in Capital Form. ● Presence of (*) in the beta carbon
● It has two chiral carbons.
GLYCINE
What makes the beta carbon of isoleucine special than the
other carbons?
Answer: It is the second chiral carbon.

● Side Chain: Hydrogen (Non-Polar)
○ Glycine is difficult to classify due to its
hydrogen side chain; which is why it is
considered as non-polar.
● Glycine is the only amino acid whose alpha carbon is
achiral.
○ Compounds with chiral centers are optically
active. Therefore, glycine is not optically
active (inactive).
○ Optically Active - can rotate a plane of
polarized light.
● Glycine is the smallest amino acid.
○ The side chain is only hydrogen.
For most amino acids that have only one chiral carbon,
how many isomers are possible for this amino acid?
Answer: 2
Using the Isomer formula = 2n
Where n is the number of chiral carbons
IMPORTANT:
● For Alanine, Valine, Leucine and Isoleucine whose side
chains are hydrocarbons (non-polar), when they are in
aqueous environment, the tendency of the side chains is
to avoid water (since the side chains are non-polar).
● When the side chains are in proximity with one another,
they tend to coalesce together via hydrophobic
interactions.
● The alpha amino group is a primary carbon since there is
only one carbon attached to the amino group.
 BIOCHEMISTRY LECTURE
METHIONINE

● R group: Thioether Group (Sulfur in between two

carbons)

PROLINE

● Proline has a cyclic structure and part of the cyclic

structure is Nitrogen (amino group).
● The side chain bound to the alpha carbon is an aliphatic
side chain that is also linked to the amino group. GROUP B. AMINO ACIDS WITH NEUTRAL POLAR SIDE
● The alpha amino group is a secondary. CHAINS
● Ninhydrin Test - test to detect the presence of amino
acids.
○ When amino acids are treated with ninhydrin
solution and heated, it would give a purple
solution. EXCEPT FOR PROLINE which
gives a yellow solution.
Ser = Serine Cys = Cysteine
● Proline is an Imino acid.
Thr = Threonine Gln = Glutamine*
PHENYLALANINE
Tyr = Tyrosine Asn = Asparagine*

● What makes them polar is the presence of an

● R Group: Phenyl Group attached to a Methylene (CH2) electronegative atom.
group.
● When the phenyl group is removed from the structure, SERINE
Alanine is formed.

Why is it F?
Answer: Because P is already taken by Proline.
In the case of phenylalanine, it is Phonetic. ● Similar to Alanine, but the methyl group is replaced by a
hydroxyl group.
Is the side chain of phenylalanine still an aliphatic side ● When another near hydroxyl containing group interacts
chain? with them, it forms hydrogen bonds.
Answer: No, it is aromatic amino acid.
THREONINE
● There are 3 AROMATIC amino acids.
● Pi-Pi Delocalization - The special type of hydrophobic
interaction that occurs between aromatic amino acids.
● Similar to an ethyl group but the second carbon* has a
TRYPTOPHAN hydroxyl group.
● Asterisk on the Beta Carbon - Achiral carbon
○ Similar to Isoleucine
● When another near hydroxyl containing group interacts
● R group: Indole with them, it forms hydrogen bonds.
● Aromatic Amino acid
● The side chain can interact with another amino acid via TYROSINE
pi-pi delocalization.
● The side chain loses its proton at around pH of 10. IT
becomes negatively charged.
 BIOCHEMISTRY LECTURE
● The phenol group would lose its proton (ionize) when the IONIZATION OF CYSTEINE AT 8.3
pH is equal or greater than 10.46.
○ It would be charged negatively. Since it
loses a proton.
● 10.46 is not the (neutral) physiological pH. The side chain
is charged at high pH.
● It is an aromatic polar amino acid, just like phenylalanine
and tryptophan, the side chain interacts via pi-pi
delocalization when they fold. It may also form hydrogen
bonds since it also contains a hydroxyl group.
● Half of the thiol is ionized to sulfide.
● The concentration of both molecules are equal.

● The phenol group would lose its proton when the pH is

equal to or greater than 10.1.
○ At exactly 10.1, we have equimolar
quantities of the phenol and phenoxide.
● It readily undergoes redox reactions with another cysteine
What is the net charge of phenol in the figure on the left? to form a dimer which is Cystine.
Answer: -1 ● The three letter word of the ff.:
○ Cysteine = Cys
What is the net charge of phenol in the figure on the right? ○ Cystine = Cys-Cys
Answer: -2 ● The one letter word for the ff.:
○ Cysteine = C
Which of the two functional groups has a higher pK value? ○ Cystine = C-C
Answer: Phenol ● Disulfide Bond = The bond connecting the two cysteine
CYSTEINE molecules

GROUP C. AMINO ACIDS WITH CHARGED SIDE CHAINS

AT PHYSIOLOGICAL CONDITION:
● R group: Thiol / Sulfhydryl
● Similar to Serine but there is a presence of a thiol instead
of an alcohol.
● There is a pK value wherein it would release its proton at
pH equal or greater than 8.37.
● At physiological conditions (7.4), the thiol would still be ● Acidic amino acids have side chains with a carboxylate
thiol and not sulfide. group that ionizes at physiological pH. (Negative Charge)
● The thiol of cysteine becomes negatively charged (S-) ● Basic amino acids bear a positive charge at physiological
once it ionizes. pH. (Positive Charge)
○ At physiological pH, lysine is its conjugate
What would be the charge of the R group once it releases acid (-NH3+), arginine is permanently
a proton? protonated, and histidine is a weak base,
Answer: Negative because it is only partly ionized.
○ Arginine is permanently protonated because
the pka value is already very high.

In an amphoteric amino acid (can both act as an acid or base),

which functional group in an amino acid gives it its acidic and
basic character?
 BIOCHEMISTRY LECTURE
Answer: Carboxylic Acid and Amino Group
● The net ionic form of the functional groups would depend
on the pH/pKa value.
If the side chain of the amino acid has a carboxylic acid,
can we say that the amino acid is an acidic amino acid?
Answer: Yes
If the amino acid has an extra amino group, would you
consider it to be a basic amino acid?
Answer: Yes
Note:
ACID ( - charge)
● An alpha carboxylic acid has a pKa value at around 2-3,
therefore at 7.4 it is already ionized (COO-)
○ At physiological conditions it is negatively
charged.
● Kapag may dalawang carboxylic acid na negatively
charged at physiological conditions, ionized na sila at
physiological conditions.
BASIC (+ charge)
● The amino group which has a pka value at around 9-10,
therefore at 7.4 it is still protonated. They are positively
charged.
● If the basic amino acids contain an amino group in their
side chain (positively charge at physiological conditions),
the basic amino acids are positively charged at
physiological conditions.
● All of them have pLa, pKamino,pKR Side Chain values.
BASIC AMINO ACIDS
LYSINE
● R Group: Contains an Aliphatic side chain that ends with
a primary amine
What amino group is present?
Answer: Primary
● The alpha amino group (NH3+) attached to the carbon
(middle) is also a primary amino group.
○ All in all there are 2 primary amino groups
present.
What is the name of the amino group at the further right (in
red)?
Answer: Epsilon Amino group
● The pK value of the Epsilon amino group (10.54) is higher
than the pK value of the alpha amino group.
○ If lysine is titrated with NaOH, the hydroxyl
ion (OH) from NaOH would seek the most
acidic proton (pH = 0) first.
○ Order of alpha proton it seeks: Alpha
Carboxylic acid proton (2.16) → Alpha
Amino proton (9.06)
○ The last proton to be titrated would be from
the Epsilon Amino Group.
In the structural formula of lysine, what is the net charge
of Lysine at physiological pH?
Answer: +1
ARGININE
● The reason for giving R for anginine is due to phonetics.
● R Group: Guanidino
● Due to the high pK value of guanidino, its arginine is said
to be always positive.
○ Due to the presence of high pK value of the
side chain and it is very basic.
● Can also be called as Guanidinium Ion.
 BIOCHEMISTRY LECTURE
Ionic Form: ACIDIC AMINO ACIDS
ASPARTIC ACID

● “Aspardic” acid tawag sa ibang book dan

● When titrated, the first proton to go is from the Alpha ○ D is due to phonetics.
Carboxylic acid → proton from Alpha Amino → proton ● Net charge in physiological conditions: -1
from the side chain (guanidino).

HISTIDINE GLUTAMIC ACID

● R Group: Imidazole Ion Form: Imidazolium Ion

Why E for glutamic acid?
● When titrated, the first proton to go is from the Alpha
Answer: Assumption nya raw is kasi next daw ng d is e wtf
Carboxylic acid → proton from imidazolium ion → proton
lamaw
from Alpha Amino group.
● Net charge in physiological conditions: -1
○ The Imidazole (Ring) has a lower pK value
than the amino group.
BOTH ASPARTIC AND GLUTAMIC ARE negatively charged
at physiological conditions
Explanation: Has a lower pK than the alpha amino group
unlike the first two where the last proton to go is from the side
RECALL: Asparagine and Glutamine
chain. Dito, the ring would be deionized first before the alpha
amino group. Considered as a basic amino acid with a pK
value of the side chain in the acidic range. Kaya lang sya
considered as basic is because of the extra amino group in the
side chain.

● At physiological conditions, at 7.4, Histidine is 60%

ionized.
○ That is why it is found in the most active site
of enzymes because it can act as an acid or
base.
○ It is involved in the relay of protons.
○ It can quench in the basic form or it can
release proton in the acidic form.
● The side chain of aspartic acid and glutamic acid can
readily react with an amine to form an amide, particularly
asparagine and glutamine.
○ Asparagine - amide form ng aspartic acid
○ Glutamine - amide form ng glutamic acid
● In their acid form, the side chain is negatively charged but
when they are converted into the amide form, they
become chargeless at physiological conditions and polar.
● Difference between these two amides is that glutamine is
one methylene longer than Asparagine. Same as
glutamic acid, it is one methylene longer than aspartic
acid.
 BIOCHEMISTRY LECTURE
IN SUMMARY: Recall: The 20 amino acids are the common amino acids
Important structural features: because they are genetically encoded. These amino acids are
1. All 20 are ɑ-amino acids. coded by specific codons in the genetic code (64 codons and 3
● Why ɑ? - Their amino and carboxyl group are of the 64 are the stop codons).
attached to the alpha carbon. ● The 21st and 22nd amino acids are encoded by one of the
2. For 19 of the 20, the ɑ-amino group is primary; for proline, stop codons.
it is secondary. ● Selenocysteine is encoded by UGA which is one of the
● Proline is a cyclic structure, part of the ring is the stop codons.
amino group. ● Selenocysteine is actually found in a group of proteins
3. With the exception of glycine, the alpha carbon of each called selenoproteins which are involved with
amino acid is a stereocenter (chiral), the all have only one detoxification processes.
chiral carbon. ○ Antioxidant activity
4. Isoleucine and threonine contain a second stereocenter (β
carbon is present). PYRROLYSINE (22nd Amino Acid)
● Lysine whose epsilon amino
SUMMARY OF THE AMINO ACIDS AND THEIR LETTER group is attached to an pyrrole
SYMBOLS through an amide bond.
● Abbreviated as Pyl or O
● Encoded by the stop codon
UAG
● Is used in the biosynthesis of
protein in some methanogenic
bacteria and archaea.

BIOLOGICALLY ACTIVE AMINO ACID DERIVATIVES

● Compounds derived from amino acids and undergone
some reaction to be converted to these derivatives.

● Amino acid is not sure if it is an asparagine or aspartic

HISTAMINE
acid pag (asX) OR (glX) for glutamine or glutamic acid.
● A potent vasodilator, which is released as part of the
● In order to know/determine the amino acid composition,
immune response.
the protein has to be hydrolyzed.
○ During an allergic reaction, you take
○ If the protein has been hydrolyzed by acid
histamine.
then nag-apper for example yung
asparagine/aspartic acid.
○ The one who did the experiment may not be
sure if aspartic acid ba yon or asparagine
that has been converted to aspartic acid.
○ Once hydrolyzed and the catalyst for
hydrolysis is an acid, the amides are
converted into its acid form. After getting the ● Derived from Histidine.
results and it is aspartic acid, in some cases How does it differ from Histidine?
the one who did the analysis may not be
sure if it is really aspartic or glutamic acid but
in its amide form.
Answer: Alpha carboxylic acid is missing
st
SELENOCYSTEINE (21 Amino Acid) ● Decarboxylation - reaction where carboxylic acid is
removed and released as carbon dioxide
● (Sec, U, in older publication also as
Se-Cys)
○ It is a modification of Cysteine
● Encoded by the stop codon UGA
○ One of the stop codons.
Difference between Cysteine and
Selenocysteine?
Answer: Sulfur is replaced with Selenium
 BIOCHEMISTRY LECTURE
𝜸-Aminobutyric acid (GABA) SEROTONIN
● A neurotransmitter that is made in the brain, and has ● The key hormone that stabilizes our mood, feelings of
anti-seizure and anti-anxiety effects. GAB works by well-being, and happiness. It enables brain cells and
blocking brain signals (neurotransmissions). other nervous systems cells to communicate with each
other.
● Serotonin also helps with sleeping, eating and digestion.

● Derived from Glutamic Acid

● Derived from Tryptophan.

● The carboxylic acid has a higher priority than the amino
group which makes it the point of reference (alpha).
● Gamma because the gamma carbon is attached to an
amino group.
● Butyric because there are 4 carbons that has carboxylic
acid.
● Undergoes process of decarboxylation and deamination
● The indole ring is hydroxylated and it is decarboxylated.
MELATONIN
● A hormone primarily released by the pineal gland at night,
and has long been associated with control of the
sleep-wake cycle.

THYROXINE
● The main hormone secreted into the bloodstream by the
thyroid gland. It plays vital roles in digestion, heart and
muscle function, brain development and maintenance of
bones.
● Derived from Tryptophan.
Fun Fact: The tryptophan content of milk is high!

● Derived from Tyrosine.

DOPAMINE
● A neurotransmitter in the brain which is released when
your brain is expecting a reward.

How did Dopamine come from Tyrosine?

Answer: The removal of the carboxylate through carboxylation
and hydroxylation of the phenol ring.
 BIOCHEMISTRY LECTURE
ADRENALINE
● Tyrosine and Phenylalanine are precursors to
norepinephrine and epinephrine (adrenaline),
Epinephrine is known as the ‘flight or fight’ hormone.
● It starts from phenylalanine which is hydroxylated to
become tyrosine. Tyrosine is further hydroxylated to
become L-dopa and decarboxylated to become
Dopamine. Lastly, two reactions to become adrenaline
(epinephrine)
● Adrenaline is the hormone released when you are under
stress.
CITRULLINE AND ORNITHINE
● Looks like amino acids, but they are not considered as
amino acids.
● But they are the precursor for the synthesis of other
molecules (e.g. Nucleotides and heme).
● Metabolic intermediates (arginine, ornithine, and
citrulline in the urea cycle)
○ They are metabolized in the urea cycle
(together with arginine).
● Urea cycle - a method/pathway that releases the amino
group of proteins in the form of urea.
○ Urea can then be excreted as a water
soluble compound in the urine.
○ One way of getting rid of the amino group of
the nitrogen containing compounds.
MODIFIED AMINO ACIDS IN PROTEINS
Post Translational Modification
● Some proteins have amino acids that are modified after
synthesis.
● Post Translational Modification - After a protein is
synthesized, some of these amino acids are modified
depending on the function of the protein.
○ Serine, threonine, and tyrosine can be
phosphorylated.
■ In order to regulate the activity of
the protein (on or off). See meaning at the
bottom
○ δ-Carboxyglutamate (prothrombin),
4-hydroxyproline (collagen), and
5-hydroxylysine (collagen)
What is common to these three amino acids (Serine,
threonine, and tyrosine)?
Answer: A Hydroxyl group which can be phosphorylated.
● Phosphorylation/Dephosphorylation - mechanism for
proteins for activating a pathway/mechanism/activity.
Example:
Enzymes - catalysts that accelerate enzymatic activity
● The majority are proteins but the activity of the
enzyme cannot always be active.
● Some enzymes have to be switched off which means
that their activity must be inhibited.
● One way of activating or deactivating is through
phosphorylation (active) or dephosphorylation
(inactive).
What do you call the carboxylate of the side chain of
glutamic acid?
Answer: δ-Carboxyglutamate
● The gamma carbon of the glutamic acid is attached to 2
carboxylate groups.
● The charge of the side chain is -2 which is important for its
role in the blood clotting process (e.g. Prothrombin)
○ -2 charge ng gamma-carboxyglutamate kasi
dalawang negative (-) charge yung nasa side
chain nya
● Prothrombin - has a key glutamate residue that is
carboxylated at the side chain.
● Bidendate: bi (two), date (negative) which has 2 negative
charges that can chelate calcium ion (2+).
○ It can quench calcium ion (one of the
reactions in the blood clotting process).
● 4-hydroxyproline (collagen) and 5-hydroxylysine
(collagen) - involved in collagen modification.
○ Both are hydroxylated so that the collagen is
strengthened by additional hydrogen
bonding (interstrand hydrogen bonding) to
make it stronger.
 BIOCHEMISTRY LECTURE
MAJORITY OF ɑ-AMINO ACIDS HAVE THE
L-CONFIGURATION AT THE ɑ-CARBON
Do amino acids contain chiral carbon?
Answer: Yes,
● In most cases it has one chiral carbon. (except for
two amino acids)
● If it has one chiral carbon, it exists in two isomeric
forms (L and D configurations); the majority of these
amino acids are in L configuration.
● For naturally occurring proteins, the majority of these
amino acids are in L configuration.
AMINO ACID STEREOISOMERS
● Because the ɑ-carbon (chiral carbon) is attached to four
different groups, they can exist as stereoisomers.
○ Except glycine, which is the only non-chiral
standard amino acid.
● They exist as D- and L- in comparison to glyceraldehyde
which is the reference compound for optical isomers.
○ D or L is used to indicate the similarity of the
arrangement of atoms around the molecule’s
asymmetric carbon to the asymmetric carbon
of the glyceraldehyde isomers.
● Chirality has a profound effect on the structure and
function of proteins.
● The molecules/stereoisomers are mirror images of one
another, or enantiomers.
● They cannot be superimposed over one another and
rotate plane, polarized light in opposite directions (optical
isomers)
○ Majority of the Naturally occurring proteins -
L-configuration
● They are optically active.
ENANTIOMER WITH ANTI-INFLAMMATORY ACTION
● When it is naturally synthesized and nature has a way of
being stereospecific in terms of its synthesis, they produce
only L amino acid except for a few proteins.
Example:
Peptide in the peptidoglycan (bacterial cell wall)
● The peptide in peptidoglycan of the bacterial cell wall has
the amino acids presumably it is for their protection.
● L amino acids turn into D in disease conditions. (In some
articles na nabasa ni ma’am)
● For the artificially synthesized compounds, it is difficult to
separate when they are synthesized as they are in a
racemic mixture (both isomers are present in one
mixture). It is quite difficult to separate them (e.g.
Ibuprofen, Vitamin E)
○ May inactive isomers to.
THALIDOMIDE ENANTIOMER WITH SEDATIVE ACTIVITY
● A problematic racemic mixture.
● Medicine for morning sickness for pregnant women.
● Thalidomide was given to them because it has a sedative
effect.
● However, the other isomer has a teratogenic activity, it
can cause malformation of the fetus.
● Many children in the 1960’s, like the babies pictured
above, were born with phocomelia as a side effect of the
drug thalidomide, resulting in the shortening or absence of
limbs.
 BIOCHEMISTRY LECTURE
AMINO ACIDS IN SOLUTION EXIST IN DIPOLAR FORM A comparison of pH in terms of their concentration values
(ZWITTERION)
Recall: Zwitterion
● Has two charger (positive and negative charges)
● The net charge is 0.
● The form wherein the positive charge is equal to the
negative charge.
● Amino acids exist in different ionic forms. It's not only the
dipolar/zwitterion but the exact ionic form of the amino
acid would depend on the pH that they are in.

Graph: Equivalence of OH- against pH

The Reaction of 2 functional groups with ionizable protons

( ɑ-COOH and ɑ-NH3)

Pink: Based on the structure, the charge is +1

Blue: Based on the structure, it is Electrically neutral, 0
Green: Based on the structure, the charge is -1
Are they the same in terms of ionic forms?
Answer: NO

Based from the graph,

● When the pH is 0 in a very acidic solution, both amino and
carboxylic acid are protonated

In terms of concentration, what is the % of the +1 ion?

Definition of a pKa Answer: 100%
pKa ● In time, the concentration decreases because +1 is being
● Gives the strength of an acid. converted to the Zwitterion.
● “At what pH would it release its proton?” ● When pH increases, +1 decreases because it is being
● It is better to define them based on the bronsted lowry converted into the zwitterion.
(capability of releasing a proton).

Based on the graph, how would you define a pKa value?

Answer: The pH at which 0.5 equivalents of OH- has been
added.

Example:
A weak acid is titrated with a base (OH-), if 0.5 OH has been
added, would all of the HA be converted to A-. Would the 0.5
equivalents convert HA to A -?
Answer: No, half lang ng equivalent

● When the pH is equal to the pKa of the weak acid, half of it

is converted to its conjugate base.
● When the pH is equal to its pKa, both forms (acid and
conjugate base) are present.
○ The ration of the two is equal to 1.
At the intersection point (red circle), what can you say
about the concentration of the two?
Answer: They are equal. At this point, the pH is equal to the
pKa of ɑ-COOH. (The ions +1 and 0 are present 50:50)
● When the +1 is converted to 0, what is removed/ionized is
the proton of the carboxylic acid (released).
● The reason why it is ionized off, the pH is becoming equal
to its pKa value.
● Concentration are equilibrium at intersection of graph
points
 BIOCHEMISTRY LECTURE
Is the intersection of the graph equal to the pKa value of ● Majority of amino acids have only 2 pKa values (based
the alpha carboxylic acid? from the previous given data since the start). ( ɑ-COOH and
Answer: Yes, pH is equal sa pKa ng alpha carboxylic acid ɑ-NH3)
● As the pH increases, the concentration of +1 decreases ○ 1 for the ɑ-carboxylic acids (ɑ-COOH) whose
and the concentration of the Zwitterion increases. pK value is only around 2-3
● There will come a point wherein their concentrations will ○ 1 for the ɑ-amino group (ɑ-NH3) whose pH
be equal and hence have a ratio of 1. ranges from 10-11
● Until such time that all the +1 will be converted to 0 ● There are amino acids that have ~3 pK values, ung third is
wherein the concentration of the Zwitterion becomes 1 and the pK values of the side chain.
all +1 is consumed.
● Concentration of zwitterion is 100% until the pH
approaches the pKa value of the alpha amino group. So at
this point (2nd intersection), concentration of the two ions
0 and -1 are equal until such time that all of the 0 ions are
converted to -1.

How would you compute the pH at which the Zwitterion

exists 100%?
Answer: By getting the average of the two pKa values (the
midpoint of the two pKa values).
Is it correct to say that the exact ionic form of the amino
acid would depend on the pH wherein it is dissolved in?
Answer: YES
TABLE 5.2 pKa Values for the Ionizing Groups of the Amino
Acids
ISOELECTRIC pH
● Going back here (Graphs), the pH where the zwitterion
exists 100% is called the isoelectric pH.
● The isoelectric pH is computed as the midpoint of the two
pKa values.
● You can readily compute for the isoelectric pH when you
look at the table of those with only two pKa values.

● For those with three pKa values, you need to average 2 of

the three depending on where the zwitterion is.

*The last column of the pK values were already discussed in

previous discussions.

IONIC FORMS OF ALANINE
At 2.3, what is the ionic form of alanine?
First Reaction:
● The first reaction would happen when the pH is equal to
2.3 (ɑ-COOH) turning it to a carboxylate.
Charge of Structure A:
Charge of Structure B:
Ionic Forms of Alanine at
2.3
● Net charge:
0+1
2
= + 0. 5
Second Reaction:
- Charge of C: -1
Charge of Structure B:
Charge of Structure C:
BIOCHEMISTRY LECTURE
Ionic Forms of Alanine at Two forms
9.7 ● B (0) and
● C (-1)
*present at 50:50 ratio
● Net charge:
0 −1
2
= − 0. 5
● When the pH is equal to 2.3, the ions present are +1 and.
● When the pH is equal to 9.7, the ions present are 0 and -1
● To compute pH where the Zwitterion (0) is 100%, you get
the midpoint of the two pK values.
2.3 + 9.7
𝐼𝑠𝑜𝑒𝑙𝑒𝑐𝑡𝑟𝑖𝑐 𝑝𝐻 (𝑝𝐼) = 2
= +6
At pH 6, structure B is present 100%
TITRATION OF AMINO ACIDS
● Technique to determine the concentration of an acid/base.
○ Because amino acids have titratable groups,
their amino form can be titrated
● Free amino acids contain ionizable groups.
● The ionic form depends on the pH.
● When amino acids have no net charge due to ionization of
+1
both groups, this is known as the isoelectric point (pH)
and can be calculated using:
0; Zwitterion Form of Alanine 𝑝𝐾1 + 𝑝𝐾2
𝐼𝑠𝑜𝑒𝑙𝑒𝑐𝑡𝑟𝑖𝑐 𝑝𝐻 (𝑝𝐼) = 2
Two forms *only if you have 2 pK values
● A (+1) and
● B (0) A. TITRATION OF ALANINE
*present at 50:50 ratio pH against equivalence of OH
How many equivalents of OH are needed to fully
deprotonate alanine?
Answer: 2 equivalence points
First equivalence point (pK): 2.3
Net charge of Alanine at low pH: +1
● When 0.5 equivalents of pH is added,
the pH is equal to the pK of the
ɑ-COOH. At that point, the 0 and +1
0 are present and their ratio is equal to 1
which means that their concentration is
-1 equal.
 BIOCHEMISTRY LECTURE
● When another 0.5 equivalents of OH- is added, such that B. TITRATION OF GLUTAMIC ACID
the total is already equal to 1, all the +1 are converted to
0. Hence, you only have the Zwitterion.

● Another 0.5 of OH- is added so that the total is already

+1.5 (hindi ito charge, equivalents lang to). The pH is
already equal to the ɑ-NH3.

At that point (9.7), how many ions are present?

Answer: 2 ions (0 and -1) How many equivalents of OH- are needed to fully
deprotonated glutamic acid?
Answer: 3 since there are 3 pK values

Sa tatlong pK values, sino ang may pinakamataas na pK

values?
Answer: Alpha Amino group

If not given, how to get the pK values of the three?

Answer: Check the corresponding values at the pH axis.
Check equivalence points at: (0.5, 1.5, 2.5)
What is the net charge when the pH is at 9.7?
Answer: -0.5 To get pH, 4.24 + 9.67 / 2 = 6.96
Pattern: +1, 0, -0.5, -1 At pH 0, what is the charge of glutamic acid?
Answer: The starting charge at pH 0 is +1 due to the alpha
When the pH is already 14, what is the net charge of amino group.
Alanine?
Answer: -1 At first equivalence point:
● OH is added, hence the pH increases. When 0.5
What if you only have the curve and the pK values are not equivalents of OH is added, the pH is equal to the pK
given, how would you know the pK values? value of the ɑ-COOH?
Answer: Check corresponding point in pH axis :DD ganun din ● At 0.5 equivalents, the ions present are +1 and 0. Hence,
gawin mo sa amino :DDD the net charge is +0.5.
0 −1
*red line = − 0. 5
2
At second equivalence point:
● The pKa value of the side chain is
reached after 1.5 addition of OH-.
● At 4.25, the 0 and -1 ions are present.
● The mid-point of 2.19 and 4.25 has a net
charge 0 (Zwitterion).
2.19 + 4.25
𝐼𝑠𝑜𝑒𝑙𝑒𝑐𝑡𝑟𝑖𝑐 𝑝𝐻 (𝑝𝐼) = 2
= + 3. 22

Would that form of Alanine/any amino acid exist in any At third equivalence point:
pH? Would that ion be possible in nature? ● After adding 2 equivalents of OH-, you have only -1.
Answer: No. Di pwedeng protonated si
COOH and deprotonated na si amino group. How would you compute for the pH in which the -1 ion
exists 100%
Wag na wag isusulat na si COOH ay still Answer: Get the average of 4.25 and 9.67
acid while the amino group is 4.25−9.67
= 6. 96
2
deprotonated.
 BIOCHEMISTRY LECTURE
Structure of Glutamic acid with the net charge of -1: TITRATION OF HISTIDINE
● Charge of Amino Group: Positively Charged
● Charge of COOH: Negatively Charged
● Charge of Side Chain: Negatively Charged

● Para maging negative 2, modify the structure by making

the amino group deprotonated (NH2).
● Notice that the pI of an acidic amino acid is way below 7. It
is in the acidic region (3.22).

● It requires 3 equivalence of OH to be fully deprotonated.

● What is the charge at pH 0: +2
○ The carboxylic acid is protonated = w/o
charge
○ The imidazole ring is protonated.
○ The alpha amino group is protonated.
● After adding 0.5 equivalents of OH, the pK value is
reached.

Whose pKa value is 1.82?

Answer: Alpha carboxylic acid

What are the ions present at pKa 1.82?

Answer: +2 and +1

● After adding an additional 0.5 equivalents of OH- such that

the total is already 1, all the +2 are converted to +1.
● Then it reaches the side chain, the pKa value of the side
chain is 6.0 (at 1.5 equivalents of OH-).

What are the ions present at pKa 1.82?

Answer: +1 and 0
● The starting charge at pH 0 is +1 because of the alpha
amino group and the side chain and the alpha carboxylic ● Compute for the pH at which the +1 ion exists at 100%,
acids are without charge because they are protonated. get the average of 1.82 and 6.00
1.82−6.00
2
= 3. 91

● After adding a total of 2.5 equivalents of OH-, the ions 0

and -1 are present.
● At the 2.0 equivalents, the Zwitterion is present with a
charge of 0.
6.00 + 9.17
𝐼𝑠𝑜𝑒𝑙𝑒𝑐𝑡𝑟𝑖𝑐 𝑝𝐻 (𝑝𝐼) = 2
= + 7. 585
 BIOCHEMISTRY LECTURE
● For histidine, mauuna side chain kesa sa alpha amino Example:
group. Paper with buffer soaked in pH of 7
● The Imidazole ring would release its proton before the
alpha amino group. (important in giving structure)

Anode Cathode
Trick:
● For an acidic amino acid, to get the isoelectric pH, you get
● Cathode is negatively charged because cations move
the first two pK values.
towards the negatively charged electrode.
● For a basic amino acid, to get the isoelectric pH, you get
● You have a solution that is made up of aspartic acid,
the last two pK values.
alanine and lysine and the solution is placed in the middle
of the paper strip, when connected to a power supply w/
electrical supply,

Which of the three at pH 7 would move towards the

anode?
Answer: Aspartic acid
Aspartic Acid (D)at pH 7 charge : -1 (towards anode +)
Lysine (K) at pH 7 charge: +1 (towards cathode -)
Alanine (A) at pH 7 charge: 0 ( just stay since it is electrically
neutral at pH 7)

FORMATION OF PEPTIDE BOND

Peptide Bond
● The bond connecting the amino acids, peptide, protein
● The peptide bond is due to the reaction of the carboxylate
of one amino acid and the amino group of the next amino
acid.
● A condensation reaction that releases water.
Lysine and Arginine have the same trend.
● In organic chemistry, the peptide bond is an amide bond.
Histidine is different.
● In protein chemistry, the amide bond is a peptide bond.

ELECTROPHORESIS
Electrophoresis
● The process of separating compounds on the basis of
their electric charge
● This is like chromatography wherein there would be
movement of compounds based on electrical charge.
○ Electrophoresis of amino acids can be
carried out using paper, starch, agar, certain
plastics, and cellulose acetate as solid
supports (stationary phase)
○ In paper electrophoresis, a paper strip
saturated with an aqueous buffer of
predetermined pH serves as a bridge
between two electrode vessels.
■ Take note: the paper which is the
solid support is soaked in buffer
Image of an example of tetrapeptide
■ Basis for choosing the correct
Why?
buffer - pH should provide
Answer: The peptide is made up of four amino acids.
maximum difference in electrical
charge.
 BIOCHEMISTRY LECTURE
If there are four (4) amino acids in the tetrapeptide, how
many peptide bonds are there?
Answer: 3 peptide bonds.
Based from the picture:
● In residue 1, the carboxylate reacts with the amino group
of residue 2 amino acid forming a peptide bond. The same
goes for residue 2,3 and 4.
● A peptide has polarity/direction, which means it has an n
(amino) terminal, and a c (carboxy) terminal.
○ Amino terminal (N-terminus) - amino acid
of a residue that has a free amino group.
■ Free - not bound/involved in
peptide bond formation.
○ Carboxy Terminal (C-terminus) - the
residue that has a free carboxylate group.
■ Free - not bound/involved in
peptide bond formation.
● When you are asked for the composition of the peptide,
you start with the N-terminal. Take note, the peptide is
written from left to right (in horizontal form). But, it can also
be written in vertical form.
● A peptide, if it is only written in its one letter symbol (e.g. Y
- E - G - K), it is understood that the N-terminal is
Tyrosine while the C-terminal is Lysine.
● When you are given the actual structure of the peptide,
you might be tricked, look for the terminal amino acid that
has a free amino group and a free carboxyl group. So that
the one that has a free amino group is the N-terminal and
the residue that has a free carboxyl group is the
C-terminal.
● It is possible that the peptide is written in reverse (C
terminal → N-terminal), or bottom (N-terminal) and top
(C-terminal).
Alanyltrosylaspartylglycine
Als - Tyr - Asp - Gly
AYDG
N-Terminal C-terminal
● N-Terminal - Alanine
● C-Terminal - Glycine
● In naming (full name) a peptide, the C-terminal is always
named as the parent compound of the peptide and it is
named as it is (e.g. Glycine).
● While the other amino acids before the C-Terminal are
named as the substituents of the C-Terminal.
● How do you name the amino acids as substituents?
○ Most of these amino acids end with “-ine”,
remove the “-ine” and replace with “-yl’’.
● N-Terminal amino acid has the free amino group; the
C-terminal has a free carboxyl group.
● Amino acid sequence leads directly to the protein’s native
conformation.
● In nature ( real biological surrounding), the protein would
not have a linear structure as written in the powerpoint. It
would assume its native (funcional, stable) conformation; it
actually folds into a three-dimensional structure that can
assume a specific biological activity.
● Depending on the amino acid sequence of the protein, it
would lead to its antive biological active conformation.
“Pentapeptide” - 5 amino acids
● N-Terminal: Serine
● C-Terminal: Leucine
● Name: Serylg-glycyl-tyrosyl-alanyl-leucine
 BIOCHEMISTRY LECTURE
DIMERIZATION OF GLUTATHIONE

“Pentapeptide” - 5 amino acids

● N-Terminal: Tyrosyl
● C-Terminal: Leucine
● Name: Tyrosyl-Glycyl-Glycyl-Phenylalanyl-Leucine How many amino acids are present in Glutathione
Answer?: Three
PEPTIDES WITH PHYSIOLOGICAL ACTIVITY
ASPARTAME Glutathione exists in two forms:
● Reduced (1 Peptide only)

The carboxylate that usually form the peptide

bond is the ɑ-COOH. It is the ɑ-COOH that
reacts with the ɑ-Amino group of the
next/succeeding amino acid.

The carbonyl of the receding amino acid that

● Bakit tinatawag ang “diet” coke? - may sugar substitute is bound to the amino group of the next
○ Sugar substitute - Aspartame amino acid.
Aspartame
● Di-peptide Bakit may prefix na gamma?
● Very sweet. 20 times sweeter than table sugar. Answer: It is the gamma carboxylate that reacted with the
● Problem: Some people have genetic disorders that alpha amino group of cysteine.
cannot metabolize phenylalanine (phenylketonuria).
● This sugar substitute cannot be used for preparing
products that need to be treated/processed at high
temperatures.
● N-Terminal - Aspartic Acid
● C-Terminal - Phenylalanine
○ Methyl ester - The carboxylate of the
phenylalanine is methylated; esterified with a ● Oxidized
methyl group Recall: Cysteine
Its thiol group readily undergoes redox reaction with another
cysteine molecule to form a disulfide between 2 cysteine
residues.
 BIOCHEMISTRY LECTURE
In the case of glutathione, it is known to react/quench reactive
oxygen species. It is known for its antioxidant property. In
effect, it becomes oxidized to Glutathione disulfide (GSSG).
● When it undergoes oxidation with another glutathione, it
becomes a dimer of two glutathione that are bound by
disulfide bonds (see image above).
● When it is already oxidized, it cannot function as a
reducing agent to quench reactive oxygen species.
● Fact: Oxidized Glutathione would do you more harm than
good. The one used in cosmetic stores is the reduced
glutathione.
(A) GSH Reduced glutathione
(B) Reaction of 2 GSH to give GSSG
(C) GSSG (Oxidized glutathione)
● Glutathione is a tripeptide found in most organisms and is
involved in protein and DNA synthesis, toxic substance
metabolism, and amino acid transport.
OXYTOCIN AND VASOPRESSIN
● Two related nonapeptide (9)
● Oxytocin - peptide that aids in uterine contraction and
lactation
● Vasopressin - antidiuretic hormone that regulates water
balance, appetite, and body temperature.
What brings about the cyclization of these nonapeptides?
Why do they have a cyclic structure?
Answer: In the two nonapeptides, there are two cysteine
residues that reacted to form disulfide bonds. Which resulted in
the cyclization of the nonapeptide.
The S in the peptide?
Answer: The disulfide from the two cysteine
(Cys).
● Take note: As emphasized in the
cysteine residue, if there are two
cysteine residues that are in proximity
with one another, the tendency for the
thiol groups is to undergo redox
reactions to form disulfide bonds.
Oxytocin and Vasopressin
● Their amino acid structure and composition is almost
similar except for two amino acids:
1. Amino acid at position 3
a. Oxytocin - Isoleucine (Ile)
b. Vasopressin - Phenylalanine
2. Amino acid at position 8
a. Oxytocin - Leucine (Leu)
b. Vasopressin - Arginine (Arg)
■ Arginine would have a charge (side
chain)
● These two hormones (peptides) bind to different receptors
in the brain (Different binding sites).
CARNOSINE
Name: β-Alanyl-L-histidine
● Medyo unusual ung dipeptide.
 BIOCHEMISTRY LECTURE
● Take Note: β-Alanyl
○ The amino and carboxyl groups are bound to
different carbons.
Why is it called β-Alanyl?
Answer: The carboxylate has a higher priority (based on the
numbering of carbon atoms). Therefore, the carboxylate is
used as the reference. The carbon after the carboxylate is the
alpha carbon.
● In a standard, both carboxylate and amino group are
attached to the alpha carbon. In the case of carnosine, the
amino group is attached to the β-carbon instead of the
ɑ-carbon.
POLYPEPTIDES AS POLYAMPHOLYTES (intro)
● Ampholytes - from the word amphoteric;
Example:
● When they form peptide bonds, the alpha carboxylate and
amino group would no longer contribute to the ionic form
of the peptide except for the N-terminal and C-Terminal.
● For tyrosine (N-Terminal), if we are going to count its
charge, hindi na natin macocount ung sa carboxylate, ung
sa amino group lang.
○ May charge ung amino group ng tyrosine
○ Wala nang charge ung carboxylate ng
tyrosine kasi bound na siya sa nitrogen of
the next amino acid.
● For Leucine (C-Terminal), the amino group of the
C-terminal is already bound to the carbonyl of
phenylalanine. But the carboxylate in the C-Terminal is
free and has a charge.
● Net charge of the peptide at physiological pH: 0
○ Except if you increase the pH and a group
ionizes to have a charge (Recall pKa
value of side chains).
● Majority of amino acids in a peptide, their ɑ-amino group
and ɑ-carboxylate group would not contribute to the net
ionic charge except for the TERMINALS.
POLYPEPTIDES AS POLYAMPHOLYTES
● The ionization of the individual residues would depend on
its environment.
● The character of the side chain in response to its
environment.
Example:
Glutamic Acid (3 Scenerios)
Scenario #1
● The side chain of glutamic acid in an unperturbed
electrostatic environment, will dissociate with a pKa near
4.2
● Pag walang katabi ung side chain (the side chain is not
affected by anything in its environment; unperturbed
electrostatic environment), the side chain will dissociate
with a pKa near 4.2 (usual pKa of the side chain of
glutamic acid).
Scenario #2
● When the side chain is near a (-) charged group, the pKa
of this side chain is >4.2.
● Pag ung glutamic acid residue is near a residue that is
negatively charged, there would be a tendency for it to
release its proton and hence become negatively charged.
Would the environment be favorable if there are two
negatively charged residues that are near each other?
Answer: No, they would repel each other.
 BIOCHEMISTRY LECTURE
● If this is the case, if the glutamic acid is near in proximity
with a negative charge residue, the tendency of glutamic
acid is to ionize at a pH higher than 4.2.

Scenario #3
● When the side chain is near a (+) charge dgroup, the pKa
of this side chain is <4.20
● Mas madali mag ionize kasi (+, -)

If it is near a positively charged residue, if it is ionized to

glutamate (+) would it be favorable if it is near a positively
charged residue?
Answer: Yes, it would result to an interaction between the two
residues.

Based on the structure, if this tetrapeptide is titrated with

NaOH, how many moles of OH do you think would it
consume for it to be fully deprotonated?
Answer: 4 moles

● At acidic condition, the net charge of the peptide is +2 due

● The tendency of the pKa values for those with ionizable
to the presence of 2 amino protonated amino groups.
groups would be altered in reaction to its environment.
● It would require 4 equivalents of OH in order for it to be
fully deprotonated.
○ The 4 functional groups that can be ionized
are:
■ ɑ-Amino group of glutamic acid (3)
■ Side chain of glutamic acid
(COOH) (2)
■ C-terminal carboxylic acid(Lysine) (1)
■ Side chain of Lysine (NH3) (4)

Which of the 4 would lose its proton first?

Answer: ɑ-COOH for Lysine (pKa = 2.19 based from table)

● After adding 2 moles of OH, +1 charge would exist 100%.

● The next functional group to lose a proton is the side
chain of glutamic acid (COOH, pKa = 4.25). The ions
present at 4.25 are +1 and 0.
 BIOCHEMISTRY LECTURE
● The pH in which the +1 would exist 100% is at:
1.8−4.2
2
=+ 3. 0
The +1 would exist at pH 3

● The third would be the ɑ-Amino group of glutamic acid

(pKa = 9.67)
*note mali ung graph ng titration curve ni ma’am basta 9.67
ung pKa nung
● 9.67 is when half of the ɑ-Amino group of glutamic acid
ionizes (0, -1)
4.2 + 9.67
𝐼𝑠𝑜𝑒𝑙𝑒𝑐𝑡𝑟𝑖𝑐 𝑝𝐻 (𝑝𝐼) = 2
= + 6. 96

● The last to go would be the side chain of Lysine (NH3)

(pKa = 10)

Would the amino group of glutamic acid consume

hydroxyl ion?
Answer: Yes

Based on the structure, would the amino group

(N-terminal) of glutamic acid consume 1 equivalent of pH?
Answer: Yes

Based on the structure, would the carboxyl group (Lysine,

C-terminal) of glutamic acid consume 1 equivalent of pH?
Answer: Yes

Unless the carboxylate (same as aspartame), this proton can

ionize off and can become carboxylate. The terminals, unless
they are converted, they contribute to the net ionic charge of
the peptide.
● In this tetrapeptide, glutamic acid has carboxylic acid
in its side chain and therefore it contributes to the net
ionic form of the peptide.
● Meanwhile the lysine contributes to the net ionic form
of the peptide.
 BIOCHEMISTRY LECTURE

PROTEINS: Structure and Functions

● Superfamilies - all of then has something to do w/ oxygen

● Hemoglobin - oxygen transporter
● Myoglobin- oxygen storage
● Neuroglobin - facilitates transfer of oxygen from the blood
brain barrier
Conjugated - there are other protein parts

Since may hypen before and after, hindi pa sila ung dulo (isang
part lang sila nung protein)