CHAPTER II

AMINO ACIDS

Amino Acid Structure

Amino acids contain two functional groups, a carboxylic acid group and an amino group. The
common amino acids are α-amino acids where both functional groups are attached to the same carbon
atom. If the R group is something other than a hydrogen atom, then the central carbon is asymmetric
and there will be two enantiomers (mirror images). For amino acids, it is the L-amino acids that are
biologically important, with very few exceptions. Amino acids found in proteins are normally L-isomers.

Amino Acid Classification

There are 20 common or major amino acids that are found in proteins. They are divided into groups
based on the nature of the R group. However, not every amino acid falls neatly into a category, so there
can be variations in how amino acids are classified. For instance, the glycine R-group is sometimes
classified as hydrophilic and sometimes as hydrophobic.

1. Nonpolar aliphatic R groups

The R group of these amino acids is hydrophobic, but not the entire amino acid. The R groups
are mainly hydrocarbon in nature.
 2. Aromatic R Groups

The R groups of these amino acids are aromatic and will absorb UV light. Involves with “aroma”
and has amino acids that has Benzene Rings.

Example of aromatics is Propan which is a flavor enhancer or pampagana.

3. Polar, uncharged R groups

The R groups of these amino acids are hydrophilic.

4. Negatively-charged R groups

These amino acids are acidic and contain an extra carboxyl group.
 5. Positively-charged R groups

These amino acids are basic and contain an extra basic group.

Amino acids can also be categorized as essential or non-essential. CHEAT SHEET #3

(a) Essential amino acids: These amino acids are not

synthesized in the body and referred as indispensable
amino acids. They are: methionine (M), arginine (A),
tryptophan (T), threonine (T), valine (V), isoleucine (I),
leucine (L), phenylalanine (P), histidine (H) and Lysine (L).
Sometimes histidine and arginine are referred as semi-
essential because body synthesizes these amino acids to
some extent.

(b) Non-essential amino acids: These amino acids are

synthesized in the body. They are alanine, glycine, serine,
tyrosine, glutamate, glutamine, aspartate, asparagine,
cysteine and proline.

“The difference between essential and non-essential amino acids is that essential amino acids cannot
be synthesized by the body and it has to be acquired through food. On the other hand, nonessential
amino acids are called so because they can be synthesized by the body.”
Properties of Amino Acids

“The nature of the R-group determines the behavior of amino acids.”

1. Optical isomerism: All the amino acids except glycine have at least one asymmetric carbon
atom. Presence of single asymmetric carbon atom gives rise to two optical isomers. One isomer
is the mirror image of the other isomer. If a carbon atom is linked to four different groups
through covalent-bonds then it is called as asymmetric carbon. The two mirror images of amino
acid serine are L-serine and D-serine.

Further, the optical isomers of amino acids are optically active (capable of rotating plane
polarized light). Some amino acids rotate plane polarized to left and some rotate to right.
All the amino acids present in human proteins are L-isomers. D-isomers are usually absent
but they are found in some peptide antibiotics.

Asymmetric means having

two sides or halves that are
not the same

clockwise Counter-clockwise

Light Lens SX Absorbed light

Regular light

“The visual property”

“In the plain polarized-light some of these amino acids rotate. Those that rotate the plane clockwise (to
the right) are said to be dextrorotatory (from the Latin dexter, "right"). Those that rotate the plane
counterclockwise (to the left) are called levorotatory (from the Latin laevus, "left"). Those that rotate
the plane in both clockwise and counterclockwise is called optical isomerism “

 Levoratory – functional
 Dextroratory- synthetic
 2. Acid-base or charge properties of amino acids:
Amino acids act as acids and bases. So, they are called as ampholytes or amphoteric
substances.
Acids are those compounds that give protons on dissociation. Bases are those compounds that
combine with protons.

CHEAT SHEET #4

acid
Also called ampholytes
 Amphoteric
base

hydrophilic
Example of both
 Amphipathic
is micelles
hydrophobic

anabolism
 Amphibolic
catabolism

3. Buffering action of amino acids:

Buffers are salts of weak acids and they resist change in pH when acid or alkali is added. Since
amino acids are ampholytes, they act as buffers. Ultra violet light (UV) absorption of amino acids.
Amino acids do not absorb visible light. Aromatic amino acids absorb ultraviolet light.
Tryptophan absorbs ultra violet light at 280 nm.

Chemical Reactions of Amino Acids

Peptides consist of 2 or more amino acid residues linked by alige, which is formed when carboxyl group
of an amino acid react with α-amino group of another amino acid.

A peptide bond is formed when carboxyl group of an amino acid react with α-amino group of another
amino acid. It is always accompanied by loss of one water molecule. Peptide and proteins contain an
amino (N–) terminus and carboxy (C–) terminus.

A peptide or protein is named starting with N-terminal amino acid and usually the N-terminal is located
on the left-hand side. A dipeptide consists of two amino acid residues and one peptide bond. Example is
Aspartame which is an artificial sweetener.
 Amino Acid Sequence

This is how the amino acid sequence can be used to

amino acid residues Peptide linkage- the bridge read amino acids; in this example, the amino acid
Tyrosine is linked to another amino acid residue by
linked by alige for each amino acid residue
the amino acid alginate. The linkage, also known as a
peptide linkage, serves as a bridge for each amino
ex. Tyrosine
acid. The five-peptide linkage in the aforementioned
case.

Special Functions of Amino Acids

A tripeptide consists of three amino acid residues and two peptide bonds. TRH and glutathione are 2
examples of biologically-important tripeptides.

Antioxidant- prevents oxidation of normally healthy cell

 Anti= prevents, oxidant= oxidation/oxidize----bad for cells

 RedOX reduces oxidation
 H202 are oxidants which destroys healthy cells
 Some examples of oxidants and free radicals like pollution, junkfoods, stress, etc
 BIOLOGICALLY-IMPORTANT AMINO ACIDS

The branched-chain amino acids (BCAAs) are a group

of three essential amino acids: leucine, isoleucine
and valine. They are essential, meaning they can't
be produced by your body and must be obtained
from food. BCAA supplements have been shown to
build muscle, decrease muscle fatigue and alleviate
muscle soreness.

CHEAT SHEET #5

KETOGENIC GLUCOGENIC MIXED

LYSINE (lys, K) HISTIDINE (his, H) ISOLEUCINE (ile, I)
LEUCINE (leu, L) METHIONINE (met, M) TRYPTOPHAN (trp,W)
VALINE (val, V) TYROSINE (tyr, Y)
ALANINE (ala,A) PHENYLALANINE (phe, F)
CYSTEINE (cys, C)
GLYCINE (gly, G)
THREONINE (thr, T)
SERINE (ser, S)
ASPARAGINE (asn, N)
ASPARTATE (asp, D)
GLUTAMINE (gln, Q)
GLUTAMATE (glu, E)
PROLINE (pro, P)
ARGININE (arg, R)

Key terms:

 Ketogenic – protection of the ketone body

 Ketone Body- which is the alternative source of energy where some of the primary sources of
energy are glucose and sometimes adipose or fats.
 Ketones - a type of chemical that your liver produces when it breaks down fats. Your body uses
ketones for energy typically during fasting, long periods of exercise, or when you don't have as
many carbohydrates.
 There are 3 stages in Starved State where the body makes use of ketones for energy
consumption
 Ketongenesis – synthesizing of ketone bodies
 Ketolysis- the breaking down of ketones and;
 Ketosis- which is the state of phenomenon produced by our liver, a process that happens
when your body doesn't have enough carbohydrates to burn for energy so it burns fats to
produces ketones for energy.
KREBS CYCLE - The tricarboxylic acid (TCA) cycle, also known as the Krebs or citric acid cycle, is the main
source of energy for cells and an important part of aerobic respiration. The cycle harnesses the available
chemical energy of acetyl coenzyme A (acetyl CoA) into the reducing power of nicotinamide adenine
dinucleotide (NADH).

glycolysis

Gluconeogenesis

Ketone body The production of Acetyl

CoA has two
passageways

1. Acetyl CoA converts

Ketones into ketone bodies
which aid in the
KREBS CYCLE production of
ketons. Note that
your ketone body is
your ketogenesis.
2. Acetyl CoA aids in
the primarily
function of the

Elements Energy Carriers are the of responsible for production of ATP in

the Electron Transport Chain which compose of;
Red is process
- FADH
Black is product
- NADPH
- GTP

An example of this is the ATP in the active transport of the PISO

pump which uses ATP for the transport of molecules
Key Terms:

 Glycogenesis- happens in the Fed stage it the process of storing excess glucose for use by the
body at a later time.

 Glycolysis- happens dependently (both in Starved and Fed Stage)

- it is the breaking down of glucose
- in simple word it is a process in which glucose (sugar) is partially broken down by
cells in enzyme reactions that do not need oxygen
- Glycolysis is the metabolic pathway that converts glucose, into pyruvate.

 Glycogenolysis- it is the breaking down of stored glucose if there no more sources available
- Glycogenolysis is the biochemical pathway in which glycogen breaks down into
glucose-1-phosphate and glucose.
 The difference of glycolysis and glycogenolysis is that Glycolysis is the initial stage of energy
production or the respiration. Therefore, when glucose is in excess (Fed stage), glucose converts into
glycogen and stores in muscle and liver tissues. On the other hand, glycogenolysis is the process of
breaking glycogen back to glucose during the low energy and low glucose levels (starved state)

 Fatty Acid Oxidation - Fatty acid oxidation is the mitochondrial aerobic process of breaking down a
fatty acid into acetyl-CoA units. Fatty acids move in this pathway as CoA derivatives utilizing NAD
and FAD. Fatty acids are activated before oxidation, utilizing ATP in the presence of CoA-SH and
acyl-CoA synthetase

 Blood Brain Barrier- The blood vessels that vascularize the central nervous system (CNS) possess
unique properties, termed the blood–brain barrier, which allow these vessels to tightly regulate
the movement of ions, molecules, and cells between the blood and the brain.
- can only pass ketones because it cannot make use of fats as energy (which is
some composition of glucose and adipose).

 Comatose - of or in a state of deep unconsciousness for a prolonged or indefinite period,

especially as a result of severe injury or illness.
-braindead
-vegetative state or unresponsive state

 Kussmaul respirations - are fast, deep breaths that occur in response to metabolic acidosis.
Kussmaul respirations happen when the body tries to remove carbon dioxide, an acid, from the
body by quickly breathing it out.
-Diabetic ketoacidosis is the most common cause of Kussmaul respirations.
Which is the increase of large number of ketones in our blood which makes
it acidic.

Chemoreceptor/ Area Postrema Trigger Zone

 is an area of the medulla oblongata that receives inputs from blood-borne drugs or
hormones, and communicates with other structures in the vomiting center to start
 vomiting, which causes electrolytes and fluids to be lost, which leads to dehydration,
which leads to hypovolemic shock and the transition into a coma.

CATHECOLAMINE SYNTHESIS- All catecholamines are synthesized from the

amino acid l-tyrosine according to the following sequence: tyrosine → dopa
(dihydroxyphenylalanine) → dopamine → norepinephrine (noradrenaline) →
epinephrine (adrenaline).

 These are chemical messengers that delivers signals to the

central nervous system

PAH (Phenylalanine Hydroxylase) TH (Tyrosine Hydroxylase) AAAD (aromatic L-amino DBH (Dopamine B-hydroxylase
acid decarboxylase)
F Y (Tyrosine) DOPA DA
(Phenylalanine)
(Dihydroxyphenylalanine) (Dopamine)

PENMT (Phenyl ethanolamine N-methyltransferase) The rate limiting step is the

conversion of Norepinephrine
to Epinephrine
NE E While the rate limiting enzyme
is the PENMT
(Norepinephrine) (Epinephrine)
Serotonin
syndrome
 Cofactors- helps our
enzyme do its job

Key Terms:

 Cofactors- a non-protein chemical compound or metallic ion that is required for an enzyme's role as a
catalyst (a catalyst is a substance that increases the rate of a chemical reaction). Cofactors can be
considered "helper molecules" that assist in biochemical transformations.

 Tryptophan -is an amino acid needed for normal growth in infants and for the production and
maintenance of the body's proteins, muscles, enzymes, and neurotransmitters. It is an essential
amino acid. This means your body cannot produce it, so you must get it from your diet.

 NIACIN- Niacin, also known as nicotinic acid, is an organic compound and a form of vitamin B₃, an
essential human nutrient. It can be manufactured by plants and animals from the amino acid
tryptophan.

 Serotonin 5HT (5 hydroxy tryptamine)- is a monoamine neurotransmitter. Its biological function is

complex and multifaceted, modulating mood, cognition, reward, learning, memory, and numerous
physiological processes such as vomiting and vasoconstriction

 Melatonin- is a hormone that your brain produces in response to darkness. It helps with the timing of
your circadian rhythms (24-hour internal clock) and with sleep.
 NAD+/ NADPH - provides the cell with a mechanism for accepting and donating electrons.
NAD+/NADH plays a significant role in the reactions associated with glycolysis, oxidative
phosphorylation, and fermentation.

 Hartnup Disease- is a condition caused by the body's inability to absorb certain protein building
blocks (amino acids) from the diet. Deficiency of the amino acid tryptophan is believed to account
for the symptoms associated with Hartnup disease
 B vitamins
 B1 (thiamin)
 B2 (riboflavin)
 B3 (niacin)
 B5 (pantothenic acid)
 B6 (pyridoxine)
 B7 (biotin)
 B9 (folate [folic acid])
 B12 (cobalamin)

H1 Causes “allergy” H2 Causes “gastric acid”

Urticaria- itching Which causes high

acidity
Sinusitis

Key terms:

 Histidine- an amino acid most people get from food. It's used in growth, repair of
damaged tissues, and making blood cells. It helps protect nerve cells. It's used by the
body to make histamine. Histidine supplements may help treat eczema.
  Histamine- a chemical created in the body that is released by white blood cells into the
bloodstream when the immune system is defending against a potential allergen.
 Urticaria- also known as hives, weals, welts or nettle rash – is a raised, itchy rash that
appears on the skin. It may appear on one part of the body or be spread across large
areas.

Key Terms:

 Glycine- is a building block for making proteins in the body. Glycine is also involved in
transmitting chemical signals in the brain, so there's interest in using it for schizophrenia
and improving memory.
 Porphyrin- Your body uses porphyrins to make heme. Heme is part of hemoglobin,
which is a protein in your red blood cells that carries oxygen from your lungs to the rest
of your body. It's normal to have a small number of porphyrins in your blood and other
body fluids.
 Hemoglobin- is a protein in red blood cells that carries oxygen. It has two compositions;
- Heme- pigment composed of hemoglobin
-Globin- the protein version
 Coordination Compounds- include such substances as vitamin B12, hemoglobin, and
chlorophyll, dyes and pigments, and catalysts used in preparing organic substances. A
major application of coordination compounds is their use as catalysts, which serve to
alter the rate of chemical reactions.
 Key terms:

 Glutamate- Glutamate's functions include: Learning and memory. By interacting with four
different receptors, glutamate has more opportunities to continue to have messages successfully
 and quickly sent between nerve cells. This fast signaling and information processing is an
important aspect of learning and memory.
-starting synthesis for the production of GABA and Glutathione
-major excitatory- signals that takes place in the Central Nervous System
 GABA- is an amino acid that functions as the primary inhibitory neurotransmitter for the central
nervous system (CNS). It functions to reduce neuronal excitability by inhibiting nerve
transmission.
 An inhibitory
 Glutathione- involved in tissue building and repair, making chemicals and proteins needed in the
body, and in immune system function.

Key Terms:

 Arginine- it has several roles in the body, such as assisting in wound healing, helping remove
excess ammonia from the body, stimulating immune function, and promoting secretion of
several hormones, including glucagon, insulin , and growth hormone.
 Creatine- helps to maintain a continuous supply of energy to working muscles by keep
production up in working muscles.
-helps our muscle boost energy consumption
 Creatinine- is a chemical waste product in the blood that passes through the kidneys to be
filtered and eliminated in urine.
 Urea- often considered simply a metabolic waste product, urea has two important physiological
functions outlined above: detoxification of ammonia and water conservation.
-end product of nitrogen metabolism
 Nitric Oxide- Its most important function is vasodilation, meaning it relaxes the inner muscles of
the blood vessels, causing them to widen and increase circulation.
- natural vasodilator
-endogenous vasodilator (widening of blood vessels)
- used in general anesthesia (can cause a “laughing episode” when a patient wakes
up with still effect of anesthesia)
- natural Endothelium Devised Relaxing Factor

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