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Module 2 Biochem

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Module 2 Biochem

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leafyvinetree
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REVIEW ON PROFESSIONAL SUBJECTS 1

MODULE 2: BIOCHEMISTRY & PHARMACOGNOSY


BIOCHEMISTRY Ribosome – actual site of protein
synthesis (70s = bacteria; 80s = human)
Biochemistry
Endoplasmic reticulum
 Science that deals with the
chemical basis of life Rough ER – other site of protein
 Biomolecular study synthesis

Monomer/Building Smooth ER – site of lipid synthesis


Blocks
Lysosomes – suicide sac; has hydrolytic
Carbohydrates Monosaccharide enzymes that digest foreign substances.
Lipids Fatty acids
Peroxisomes – act as detoxifier of
Proteins Amino acids reactive oxygen species or free radicals;
Nucleic acids Nucleotides responsible for oxidation of uric acid;
The Cell and its parts breaks Very long chain fatty acids.

 Structural and functional unit of all Golgi apparatus – modifies protein and
living things lipids
 Basic unit of life Organelles (‘little organs’)
Cell Membrane Organelle Function

(contains phospholipid; hydrophilic polar Ribosomes Site of CHON


synthesis
head, hydrophobic non-polar tail –
therefore they are amphiphilic) Endoplasmic reticulum CHON synthesis
(rough)
 Fluid Mosaic Model Lipid synthesis
 Properties (smooth)
1. Semi-permeable (not all can Golgi apparatus Modifies CHON and
pass through) lipid
2. Amphiphilic (amphiprotic) Lysosomes Digest foreign
 Board Exam substances
 Integral protein – embedded Peroxisomes Detoxifier of free
within the cell membrane; this radicals
could serve as gateway where Mitochondria Energy production
ions can go through this type of Centrosome Microtubule organizing
protein center (MTOC) of
(cell cycle regulation)
 Peripheral protein – animal cell, cell cycle
embedded outside the cell regulation
membrane. Act as receptor Nucleus
 Control center of the cell
 Where DNA synthesis is located
Nucleolus – site of ribosome assembly
CARBOHYDRATES
1. Aka: Polyhydroxyaldehyde and
Polyhydroxyketone
2. Building block: monosaccharides
Cytoplasm 3. Functional groups:
a) Aldehyde
 Cell contents outside the nucleus
b) Ketone
 Cytosol = Fluid part of the cell
c) Alcohol
 Organelles = small organs that
Reactions:
have its own function
1. Synthesis: Dehydration (remove
Mitochondrion – powerhouse of the cell; water) thus form a glycosidic
in charge of energy production bond/linkage similar to ether
linkage
PORLANTE, Jefferson “Tino” Aguado
REVIEW ON PROFESSIONAL SUBJECTS 1
MODULE 2: BIOCHEMISTRY & PHARMACOGNOSY
2. Degradation: Hydrolysis
Classification according to the
number of monomer units
Unit Type/Class
Monosacchari Always 1 Always 1
des
Disaccharides Always 2 Up to 2
Oligosaccharid 3 – 10 1 or more
es
Polysaccharid > 10 1 or more
es

Glu + Glu + Glu = 3 units/ 1 class


Glu + Fru + Gal = 3 units/ 3 class

Forms of Isomerism
 Enantiomers (mirror images and
non-superimposable)
 D and L isomerism
 Anomers
 Forms = α (OH is at lower
position), β (OH is at higher
position)

Reducing Sugars
 Rule:
 Monosaccharides =
reducing sugars
 Structures =  Disaccharides = reducing
 Mutarotation = inversion of sugars except sucrose and
OH group at the anomeric trehalose
Carbon  Polysaccharides = non-
 Epimers = same all except in 1 reducing sugars
Carbon (not C1)  Tests:
 Tautomers 1. Fehling’s test
 Aldose-ketose isomerism 2. Benedict’s test
3. Barfoed’s test (can be used
Pyranose Furanose in differentiation of
(6 membered ring) (5 membered monosaccharide and
ring) disaccharide)
Polysaccharides
Beta  Contain > 10 monomer units
 “Glycans”
 2 types:
Alph
 Homopolysaccharides (one
a
type of sugar is produced
after hydrolysis)
Glucosan = after
hydrolysis, the product is
Glycosidic pure glucose
bond Ex. Starch, glycogen,
Epimers cellulose

PORLANTE, Jefferson “Tino” Aguado


REVIEW ON PROFESSIONAL SUBJECTS 1
MODULE 2: BIOCHEMISTRY & PHARMACOGNOSY
Fructosan = the product is “Exergonic” “Endergonic”
pure fructose Release
Ex. Inulin Examples “-lysis” “-genesis”
Glycolysis, Glycogenesis,
 Heteropolysaccharides
Glycogenolysis Gluconeogene
Gums, mucilages Proteolysis sis,
Glycosaminoglycans Lipogenesis
(GAGs)
Homopolysaccharides
 Same type of monomer units *Amphibolism = intermediate reaction of
 Types catabolism and anabolism; Krebs
 Glucosan cycle/TCA (tricarboxylic acid) cycle
 Fructosan Applying principles of Thermodynamics in
Heteropolysaccharides exergonic and endergonic:
 Contains 2 or more types of
G < 0 (exergonic)
monomer units
 Examples of GAGs G > 0 (endergonic)
1. Heparin Glycogenolysis vs Glycogenesis
2. Heparan
Parameter Glycogenoly Glycogenesi
3. Chondroitin sis s
 Examples of Gums
Description Glycogen → Glucose →
 Acacia gum Glucose Glycogen
 Xanthan gum
Type of Catabolic Anabolic
 Dextran reaction reaction reaction
Glycosaminoglycans
Hormone Glucagon Insulin
1. Chondroitin SO4 – most common regulator
and abundant; found in human (Epinephrine, (Amylin,
Cortisol, Incretin)
body – cartilage, ligaments, growth
(can be used
aorta, tendons) hormone)
in
2. Keratan SO4 – most management
heterogenous in Diabetes
3. Dermatan SO4 – present in skin, mellitus)
heart valve, blood vessel Glucose level Hyperglycemi Hypoglycemia
4. Hyaluronic acid – unsulfated and a
not covalently bonded; used as
lubricant, shock absorber
Bioenergetics
5. Heparan SO4 – only extracellular
GAG; located in cell surface Paramete Substrate Oxidative
r Level Phosphorylati
6. Heparin SO4 (anticoagulant) Phosphorylati on
Biochemical Metabolism on
 Metabolism Oxygen No Yes
 Totality of chemical requireme
reaction that occur in an nt
organism ATP Yes (1 ATP) Yes (2 – 3 ATP)
 Biochemical Metabolism generation
1. Catabolism Examples PEP → Pyruvate Pyruvate → Acetyl
CoA
2. Anabolism Through the
enzyme, pyruvate Through the
3. Amphibolism kinase enzyme, pyruvate
Metabolism dehydrogenase
There’s formation
Parameter Catabolism Anabolism of ATP Intermediate
process
Keywords “Break down” “build-up”
NADH will be
(Complex to
produced
simpler)
Enzyme Kinase Dehydrogenase
Exerts Gain (absorbs)
involveme
(releases) energy  FADH2 = 2 ATP
nt  NADH = 3 ATP
energy

PORLANTE, Jefferson “Tino” Aguado


REVIEW ON PROFESSIONAL SUBJECTS 1
MODULE 2: BIOCHEMISTRY & PHARMACOGNOSY

GLYCOLYSIS
Old name of glucose: Glycose
Important precursor: Glucose
Aerobic: Glucose → Pyruvate

 Embden-Mayerhoff pathway
 End product:
 Aerobic: Pyruvate
 Anaerobic: Lactate
 Cellular location: Cytosol
Enzyme Involvement: Glycolysis
 Kinase: ± PO4-3 (addition or removal
of phosphate)
 Isomerase: Aldose ↔ Ketose
Aldose Ketose
Glucose Fructose
Glyceraldehyde Dihydroxyacetone
(3C) (3C)

 Aldolase: number of Carbon is


divided by 2
Ex. Fructose (6 Carbon) divided by 2 = 3
Carbon (Glyceraldehyde and
Dihydroxyacetone (DHA))
 Dehydrogenase: produces ATP;
NADH producer; NADH will be NADH is transported using shuttle:
transported using G3P shuttle, G3P shuttle: 1 NADH = 2 ATPs
malate aspartate shuttle Malate-Aspartate shuttle: 1 NADH = 3 ATPs
 Mutase: change the location of the 6 – 8 ATP was produced
phosphate group Anaerobic Glycolysis
Ex. from position 3 to position 2
 Enolase: water removal; process of Oxygen is not required
dehydration  ATP production: 2 ATP
 Pyruvate becomes Lactate
 Oxygen requiring? NO
Gluconeogenesis
Glucose new formation

 Definition: formation of new glucose


 Confined in the liver, intestinal
epithelium, kidney
 Sources:
1. Glycerol
2. Amino acid
3. Pyruvate
4. Oxaloacetate
5. Sugar alcohol
Almost reversible of glycolysis
Glycolysis Gluconeogenesis
Pyruvate kinase (a) Pyruvate
reaction carboxylase
Pyruvate →
Oxaloacetate

PORLANTE, Jefferson “Tino” Aguado


REVIEW ON PROFESSIONAL SUBJECTS 1
MODULE 2: BIOCHEMISTRY & PHARMACOGNOSY
(b) PEP carboxykinase Acetyl CoA + 3NAD + FAD + GDP →
OAA → PEP 2CO2 + FADH2 + 3NADH + GTP (12 ATP
PFK reaction Fructose or 10 ATP per 1 Acetyl CoA)
bisphosphatase
reaction
Hexokinase reaction Glucose-6- 1 FADH2 = 2 ATP (1.5 ATP)
phosphatase 1 NADH = 3 ATP (2.5 ATP)
1 GTP = 1 ATP

In Glycolysis
11 steps (refer to as anaerobic), 8
reversible, 3 irreversible (if there’s
kinase, however there are 4 steps that
have kinases, 1 is reversible which is
Step 7 Phosphoglycerate kinase)

*Thiokinase (Succinyl CoA synthetase)


Step/s with NADH: 3,4,8 = 9 ATP/7.5 ATP
Step/s with FADH2: 6 = 2 ATP/1.5 ATP
Step/s with GTP: 5 = 1 ATP
Total ATP: 12 ATP/10 ATP
1 mole of glucose, how many ATPs?

Kreb’s Cycle
 Other names
1. Tricarboxylic acid cycle (TCA) Electron Transport Chain
2. Citric acid cycle  Location: Inner mitochondrial
 Occurrence: Mitochondria membrane
 Net reaction:  Final electron acceptor: Oxygen
 Partial reduction: Free radicals (O2-,
H2O2) until it reduces to H2O

PORLANTE, Jefferson “Tino” Aguado


REVIEW ON PROFESSIONAL SUBJECTS 1
MODULE 2: BIOCHEMISTRY & PHARMACOGNOSY
pumped, however 2H was utilized in
 Complete reduction: H2O reducing Oxygen which results to H 2O as
final product.
Complexes in ETC Which complex is not responsible for
Responsible for transport of electrons pumping of proton/hydrogen? Complex II
If dehydrogenase is not encountered, ATP synthase:
oxidoreductase is used
In 4H+ = 1 ATP
 Complex I: NADH dehydrogenase
For NADH
Complex
Complex I = 4H+ = 1 ATP
 Complex II: Succinate dehydrogenase
Complex III = 4H+ = 1 ATP
Complex
Complex IV = 2H+ = ½ ATP
 Complex III: Cytochrome b-c1 complex
Therefore, 1 NADH = 2.5 ATP
 Complex IV: Cytochrome oxidase
enzyme
 Complex V: ATP synthase (synthase For FADH2, found in Complex II
means to produce) Complex II = FADH2 → FAD+ + 2e
*Connecting links: 2e will be transferred to Q, Cytochrome
 Ubiquinone (Q) – mobile carrier of iii, Cytochrome C, Cytochrome IV,
electron accepted by the oxygen
 Cytochrome C Complex III = 4H+ = 1 ATP
These three can produce NADH or FADH2 Complex IV = 2H+ = ½ ATP
Therefore, 1 FADH2 = 1.5 ATP
o Glycolysis has NADH on step 6
o Krebs cycle has NADH on steps
3,4,8 BLOCKER
o B-oxidation of fatty acid Complex I Barbiturate
Oxidation (Patient could die
from respiratory
 Addition of Oxygen
depression when
 Removal of hydrogen
he or she use too
 Valence increase much amount of
 Loss of electron Barbiturate)
 Substance that oxidized: Reducing
agent Complex II Malonate

Reduction Complex III BAL (British Anti-


Lewisite)
 Addition of Hydrogen
Complex IV Carbon monoxide,
 Removal of oxygen
Cyanide, Hydrogen
 Valence decrease sulfide
 Gain of electron
 Substance that reduced: Oxidizing
agent Pentose Phosphate Pathway
 Aka: Hexose monophosphate (HMP)
Shunt
 Occurrence: Cytosol
 Goals:
1. Produce ribose-5-phosphate
2. Produce NADPH (needed to
facilitate steroid and fatty acid
synthesis; maintaining the
integrity of RBC by maintaining
In every complex, there are 4H+ that can the reduced form of GSH)
be pumped. In Complex IV, 4H should be

PORLANTE, Jefferson “Tino” Aguado


REVIEW ON PROFESSIONAL SUBJECTS 1
MODULE 2: BIOCHEMISTRY & PHARMACOGNOSY
H2O2 (free radical) will attempt to Disease enzyme
hemolyze the blood Type V McArdle’s Muscle
disease phosphorylase
Type VI Hers disease Glycogen
phosphorylase
Reduced GSH → Oxidized GSH Type VII Tarui’s Muscle
(protective) (non-protective) disease phosphofructokin
ase

Oxidized GSH - it doesn’t provide Type VIII - Liver


phosphorylase
protection against hemolysis due
to free radicals.
Test for Carbohydrates
Thus, NADPH is needed to
QUALITATIVE TEST VISIBLE RESULT
maintain reduced GSH form, which
is produced via PPP. Once (Carbohydrates)
produced, the H adds to the General Test for
oxidized GSH, it will be in reduced Carbohydrates
form.  Molisch test  Purple ring
 Anthrone test (junction)
 Green/blue green
Favism (G6PD deficiency) –
Test for Pentoses
patient lacks Glucose-6-phopshate
dehydrogenase, which is helpful in  Tauber’s  Cherry red
Benzidine test
PPP. No G6PD, decrease PPP,  Bial’s orcinol test  Blue green
decreased production of NADPH,  Tollen’s  Red color
glutathione can’t be converted Phloroglucinol test
back to its reduced form. Test for Ketoses
 Seliwanoff’s test  Red color
Primaquine, Sulfonamides =  Tauber’s Amino  Bright reddish
agents that will be able to guanidine test purple
hemolyze the RBC Test for Reducing
Sugars
 Brick red
Patients with favism suffer from  Fehling’s A – precipitate
hemolytic anemia CuSO4
 Fehling’s B – NaK
3. Interconvert hexose and pentose tartrate  Brick red
 G6PD deficiency  Benedict’s test precipitate
 Aka Favism Test to differentiate
 Result: Hemolytic anemia monosaccharide from
disaccharide
Glycogen Storage Disease
 Barfoed’s test  Brick red
GSD Type Other name Enzyme precipitate
deficient
Mucic acid test
Type 0 - Glycogen
 Specific test for Mucic acid – the only
synthase
Galactose insoluble disaccharide
Type I Von Gierke’s Glucose-6-  Galactose + HNO3 in water
disease phosphatase (Ia) = Galactaric acid
(Mucic acid)
G-6-translocase
(Ib)
Type II Pompe’s α-1,4-glucosidase
LIPIDS
disease or acid maltase
Type III Cori’s Debranching  Heterogenous group of compounds
Type IIIa
disease enzyme related more by their physical rather
(α-1,6- than chemical properties
Type IIIb
glucosidase)  Important property: hydrophobic (non-
Type IIIc polar)
Type IIId
When added with water, it will result to
Type IV Andersons Branching repulsion
PORLANTE, Jefferson “Tino” Aguado
REVIEW ON PROFESSIONAL SUBJECTS 1
MODULE 2: BIOCHEMISTRY & PHARMACOGNOSY
Important Lipids Phospholipids
Saturated fats = ic  Glycerophospholipid
Unsaturated fats = eic, enic, onic  Glycerol + FA + phosphoric acid
Palmitic acid = 16:0  Sphingophospholipids/Sphingolipids
 Sphingomyelin: present in
nerves

Linoleic acid = 18:2; ω-6 dietary Sphingomyelinase: enzyme that


precursor of prostaglandin degrades sphingomyelin
Niemann-Pick disease: if sphingomyelin
will not be degraded; patient lacks
sphingomyelinase; the child may suffer
Linolenic acid = 18:3; ω-3 from early childhood death, and mental
retardation because of accumulation of
sphingomyelin
Glycerophospholipids
Arachidonic acid (Eicosanoid) = 20:4; ω-
6; precursor of prostaglandin  Phosphatidic acid + alcohol
 Serine + PA: Phosphatidylcholine
 Ethanolamine + PA:
Phosphatidylethanolamine
Simple lipids  Choline + PA: Phosphatidylcholine
 Waxes  Inositol + PA: Phospatidylinositol
 Sterols  Glycerol + PA: Phosphatidylglycerol
 Fats (TAGs) If 2 glycerol are present,
 Fixed Oils diphosphatidylglycerol
 Cardiolipin: diphosphatidylglycerol
Waxes High MW alcohol and fatty
 Which of the mentioned sterols is
acids
similar to lecithin?
Solid, except jojoba oil Phosphatidylcholine
Fats & Fats → solid, except cod liver  Other name of
oils oil Phosphatidylethanolamine: Cephalin
Fixed oils → liquid, except Correlation
Theobroma oil
 Lecithin Deficiency
Sterols Nucleus: CPPP  Lecithin is a lung surfactant
Cyclopentanoperhydrophenan  Respiratory stress syndrome
trene (common to premature babies who
lack lecithin)
Sphingolipids
 Animal: Cholesterol (wide occurring
sterol)  Ceramide = Sphingosine + FA
 Plant: Phytosterol  Precursor of glycolipids
 Sitosterol – most abundant  Sphingomyelin = Sphingosine +
plant sterol Phosphorylcholine
 Stigmasterol  Constituent of myelin sheaths
 Fungi: Ergosterol
 Feces: Coprosterol
Complex Lipids
 Phospholipids
 Glycolipids
 Sulfolipids
 Lipopolysaccharides (lipid w/ complex
carbohydrates)

PORLANTE, Jefferson “Tino” Aguado


REVIEW ON PROFESSIONAL SUBJECTS 1
MODULE 2: BIOCHEMISTRY & PHARMACOGNOSY
Glycolipids Decrease level of chylomicrons: no
option; diet control; Ezetimibe may do
 Ceramide + Carbohydrates
1. Cerebrosides = ceramide + glu/gal Dietary Lipid Metabolism
Glucocerebroside  Digestion starts in the stomach
Galactocerebroside  Lingual lipase + gastric lipase = helps
2. Gangliosides = cerebroside + sialic in increasing the metabolism of lipids
acid (n-acetyl-neuraminic acid)  Lipase = TAGs, fats
3. Sulfatide = cerebroside + sulfate  Emulsification occurs in the duodenum
Lipopolysaccharides  Bile salts (made in the liver and stored
in the gall bladder) + peristalsis →
 Polysaccharide-containing lipids
emulsification
Sulfolipids
LIPID METABOLISM
 Sulfur containing lipids (lipoproteins)
 β-oxidation:
Precursor and Derived Lipids  medium chain fatty acid
 Terpenoids = terpenes (mitochondria)
 Precursor: isoprene units  Very long chain fatty acid
 Steroids = sterols (peroxisome)
 Nucleus: CPPP Number of
 Autacoids (E.g. Prostaglandin) Carbon
 Precursor: Arachidonic acid Capric 10
 Parent: Prostonoic acid Lauric 12
 1st detection: seminal fluid
Myristic 14
4 Major Groups of Lipoproteins Palmitic 16
Chylomicron Stearic 18
 Comes from diet Arachidic 20
 Hyperchylomicronemia: Elevated
chylomicron (Type I  α-oxidation:
lipoproteinemia)  branched fatty acid
 ↑ VLDL (exogenous)
How many ATPs are formed in the β-
Low Density Lipoprotein oxidation of:
 Bad cholesterol 1. Capric acid (10C)
 Hypercholesterolemia: Elevated
LDL (Type IIa)
 Combined Hyperlipidemia (Type
IIb) = ↑ LDL, ↑ IDL
Acet = 2 carbons
Very Low Density Lipoprotein
In 10 Carbons of Capric acid, 5
 Endogenous (produced in the liver) Acetyl CoA was produced
 Hypertriglyceridemia (Type IV): ↑
Triglycerides; at risk of acute Acetyl CoA: 5
pancreatitis 1 mol Acetyl CoA = 12 ATP or 10 ATP

High Density Lipoprotein


Determine number of rounds, how
 Good cholesterol many times it was divided? Or
 ↑ HDL = decrease risk of coronary simply:
artery disease NADH or FADH2 = # of Acetyl CoA –
*Absence of HDL: Tangier disease 1=5–1=4

Decrease level of LDL: statins NADH: 4


Decrease level of VLDL: fibrates FADH2: 4
1 mol NADH = 3 ATP or 2.5 ATP
1 mol FADH2 = 2 ATP or 1.5 ATP

PORLANTE, Jefferson “Tino” Aguado


REVIEW ON PROFESSIONAL SUBJECTS 1
MODULE 2: BIOCHEMISTRY & PHARMACOGNOSY
Acetyl 8 12 96
CoA
How many In 1 mol of Subtot
was a al NADH 7 3 21
produced substance, FADH2 7 2 14
how many
ATP was TOTAL 131
produced ATP
Acetyl 5 12 60 NET ATP TOTAL ATP – 2 ATP (need 129
CoA for activation of β-
oxidation)
NADH 4 3 12
FADH2 4 2 8
TOTAL 80 How many In 1 mol of Subtot
ATP was a al
produced substance,
NET ATP TOTAL ATP – 2 ATP (need 78 how many
for activation of β- ATP was
oxidation) produced
Acetyl 8 10 80
CoA
How many In 1 mol of Subtot
was a al NADH 7 2.5 17.5
produced substance, FADH2 7 1.5 10.5
how many
ATP was TOTAL 108
produced ATP
Acetyl 5 10 50 NET ATP TOTAL ATP – 2 ATP (need 106
CoA for activation of β-
oxidation)
NADH 4 2.5 10
Lipid Metabolism
FADH2 4 1.5 6
TOTAL 66  CATABOLISM
ATP
Triglycerides (TG) = glycerol + fatty
NET ATP TOTAL ATP – 2 ATP (need 64 acids
for activation of β-
oxidation) Glycerol could undergo:

Glycerol Gluconeogenesis Glucose


2. Palmitic acid (16C) →

In 16 Carbons of Palmitic acid, 8 Glycerol Glycolysis Pyruvate



Acetyl CoA was produced
Glycerol → Glyceraldehyde → Pyruvate
Acetyl CoA: 8 Fatty acids will undergo:
1 mol Acetyl CoA = 12 ATP or 10 ATP
'
Fatty acid β oxidation

Acetyl CoA Kre b →s cycle
Determine number of rounds, how
CO2 + H2O
many times it was divided? Or
simply: Steroids → can be catabolized into Bile
NADH or FADH2 = # of Acetyl CoA – acids, Vit. D, hormones (cortisol,
1=8–1=7 estrogen, androgen)
 Not broken down completely
NADH: 7  ANABOLISM (lipogénesis – formation
FADH2: 7 of lipids)
1 mol NADH = 3 ATP or 2.5 ATP
 Formation of FA: cytoplasm
1 mol FADH2 = 2 ATP or 1.5 ATP
 Unsaturation: mitochondria,
smooth ER
How many In 1 mol of Subtot
was a al Chemical Tests (Lipids)
produced substance,
how many  Rosenheim Test – used to detect the
ATP was presence of choline
produced

PORLANTE, Jefferson “Tino” Aguado


REVIEW ON PROFESSIONAL SUBJECTS 1
MODULE 2: BIOCHEMISTRY & PHARMACOGNOSY
 Liebermann-Burchard test – most glycine is replaced by H). Glycine is
sensitive test to detect the presence the only achiral amino acid.
of cholesterol
Expected result: green, emerald green
Calories
Generate after certain chemical reaction
 1000 cal = 1 kcal  Amphoteric: carboxylic acid is
acidic, Amino group is basic, hence
 1 g CHO = 4 kcal amino acid is amphoteric (being an
 1 g Fat = 9 kcal acid and base)
 1 g dextrose = 3.4 kcal (parenteral)  Zwitterionic: presence of dipolar
 1 g ethanol = 7.1 kcal charge (has + and – charge)
PROTEINS
 Most abundant and most
functionally diverse biomolecules in
living systems
 Building blocks: Amino acids
 Bond: peptide bond
 Isoelectric (isoionic) point: pH at
Biomolecules Type of
which the amino acid is electrically
bond/linkage
neutral (0 charge)
Carbohydrates Glycosidic (ether)
Isoelectric point Considerations (pI)
Lipids Ester
Proteins Peptide Average of 2 pKas
Nucleic acid Phosphodiester  Neutral side chain: 2 pKas are given,
Protein Functions get the average
 Acidic: get the average of 2 near pKas
 Storage and Transport  Basic: get the average of 2 near pKas
 Ferritin: storage form of Iron  Ionizable group: Cysteine, Tyrosine;
 Transferrin: transport form of Iron get the average of 2 lowest pKa
 Hemoglobin: oxygen transport values
 Biological catalyst: Enzymes
(increases chemical reaction) Ex.
 Muscular contraction: contractile 1.
proteins (actin and myosin)
 Structural Proteins: collagen (most
abundant protein in the body), keratin
(found in hair and horns
A B C D
 Immunoglobulins = antibodies
1. IgM = largest among x / x
immunoglobulins x
2. IgA = secretory antibody pKa 1+ pKa3 1.88+3.65
pI = = =2.77
3. IgD = found in cell surface 2 2
4. IgG = smallest; can also be seen in
2. Tyrosine (ionizable group)
the placenta
5. IgE = responsible for allergic
reaction

Proteins
 Monomer: Amino acids
 Properties:
 Chirality: 4 different substituents
(except Glycine, because R of
PORLANTE, Jefferson “Tino” Aguado
REVIEW ON PROFESSIONAL SUBJECTS 1
MODULE 2: BIOCHEMISTRY & PHARMACOGNOSY
pKa 1+ pKa2 2.2+9.1 cycle
pI = = =5.65
2 2 Amino acid A, Q
transported to the
3. Cysteine (ionizable group)
liver
Only achiral amino G
acid
With imino group P

* Cysteine + Cysteine = Cystine (formed by


disulfide bonds)

pKa 1+ pKa2 1.7+8.3 Some notes


pI = = =5
2 2  Each amino acid has carboxyl group, a
Amino acid primary amino group (except Proline)
& side chain
Amino acid 3 Letter 1 Letter
Abbrev Abbrev Proline has imino group
 Simplest amino acid: Glycine
Cysteine Cys C
Histidine His H Amino acid Classification
Methionine Met M  Polar: R-SH, R-CONH2, R-OH
Serine Ser S NY ST QC (New York ST. Cubao,
Quezon City)
Valine Val V
Alanine Ala A
Glycine Gly G
Proline Pro P
Threonine The T
Leucine Leu L
Isoleucine Ile I

Amino acid 3 Letter 1 Letter  Nonpolar: alkyl group, R-S-R


Abbrev Abbrev
Arginine Arg R
Asparagine Asn N
Aspartate Asp D
Aspartate or Asx B (D,N)
Asparagine
Glutamate Glu E
 Acidic: -COOH
Glutamine Gln Q ac E D ic
Glutamate or Glx Z
Glutamine
Phenylalanine Phe F
Tyrosine Tyr Y
Tryptophan Trp W
Lysine Lys K

 Basic: -NH2
Must-know info H A L kaline
Aromatic amino F, Y, W
acids
Sulfur-containing M, C
amino acids
Involved in urea D
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CONJUGATE PROSTHETIC EXAMPLES
D PROTEIN GROUP
Phosphoprotei Phosphoric Casein (milk)
ns acid Ovovitellin
(egg yolk)
Nucleoprotein Nucleic acid Nuclein (cell
s nuclei)
Glycoproteins Carbohydrate Mucins
s (Vitreous
Classification of Proteins humor and
saliva)
 Simple Proteins: converted to amino
Chromoprotei Colored Hemoglobin
acids only after hydrolysis ns substance (blood)
Simple Characteristi Examples Flavoproteins
Proteins cs Lipoproteins Lipid Chylomicron
Albumins  Soluble in Serum Lecithin
H2O albumin Metalloprotein Metal Enzymes
 Coagulated Egg white s (tyrosinase,
by heat arginase,
Globulins  Insoluble in Serum xanthine
H2O globulin oxidase)
 Soluble in
dilute salt
solutions  Derived Proteins:
 Coagulated 1. + Denaturation: Denatured
by heat proteins; primary derived proteins
Glutelins  Insoluble in Glutenin 2. Progressive hydrolysis: secondary
H2O or (wheat) derived proteins
dilute salt
solution Primary Derived Proteins
 Soluble in
dilute acid  Aka as Denatured proteins
or alkali
Primary Denaturant Examples
Prolamines  Insoluble Zein (corn) Denatured
in neutral Gliadin Protein
solutions (wheat)
 Soluble in Proteans Water, Fibrin from
80% enzyme, fibrinogen
alcohol dilute acid
Myosan from
Albuminoids  Dissolved Keratin (hair myosin
only by and horny Metaproteins Acid/alkali Albuminates
boiling in tissue)
strong Elastin Coagulated Heat, alcohol Coagulated
acids (tendons and Proteins egg albumin
arteries) Cooked meat
Collagen (skin
and tendons)
Histones  Soluble in Thymus Secondary Derived Proteins
H2O histone and
 Insoluble hemoglobin  Progressive hydrolysis of protein
in dilute
NH3 Secondary Characteristics
 Basic in Denatured Protein
reaction Proteoses Highest MW group
Protamines  Soluble in Salmin and Peptones Intermediate MW
NH3, H2O, sturin (fish
dilute acid sperm) Peptides Lowest MW group
 Strongly
basic in
reaction Structural Organization
1. Primary structure
 Conjugated Proteins: protein + non-
protein portion (prosthetic group)

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 Amino acid sequence


 Bonds: Peptide bond
 Degradation: Hydrolysis
 Why needed?
2. Secondary structure
 Application:
1. Purine → uric acid
2. Protein → urea
Protein misfolding (in secondary
structure)
 Describes folding/bending of a) Alzheimer’s disease: Amyloid-β
polypeptide chain into helix/sheets b) Parkinson’s disease: α-synuclein
 Bond: Hydrogen bond
 Destroyed via Denaturation Enzymes
process  Role: catalysts (↑ rate of chemical
3. Tertiary Structure reaction)
 Are all enzymes protein? No
 Generally, YES
 Nucleic acid enzymes:
Ribozymes
Parts of Enzymes
 HOLOENZYME: active enzyme
 3-D folding pattern of a polypeptide  APOENZYME: protein portion
chain (inactive form ; active : simple
 Several bonds (hydrophobic, enzyme)
hydrophilic, ionic, hydrogen bond,  COFACTOR: non-protein portion
disulfide bond) (Vitamins act as cofactor)
4. Quaternary Structure 1. Activator
2. Coenzyme: loosely bound
3. Prosthetic group: tightly bound
 ZYMOGEN: inactive enzyme; it will
be activated once cofactor is added

Pepsinogen + HCl Pepsin


 Most complicated Trypsinogen + NaOH Trypsin



 Overall arrangement of polypeptide
chains Cofactors
 Several bonds COFACTOR ENZYME/PROTEIN
Nitrogen Metabolism Zn +2
Carbonic anhydrase

Nitrogen must be eliminated from the body Zn+2 Alcohol dehydrogenase


because it is toxic Fe +2
Cytochromes, hemoglobin
Initial step: Deamination – remove amine
NH3 is toxic to the brain; in order to prevent Cu Cytochrome oxidase
toxicity associated to NH3, it undergoes Urea +
K , Mg +2
Pyruvate phosphokinase
cycle. NH3 must be converted to urea for it to be
eliminated in the kidney. Coenzymes
↑ NH3 levels will invade the brain and will cause Vitamin Coenzyme Coenzyme
encephalopathy function
Vitamin B1 Thiamine Oxidative
pyrophosphate decarboxylati
(Thiamine)
(TPP) on
Vitamin B2 Flavin Adenine Redox
Dinucleotide reaction
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(Riboflavin) (FAD+) /Flavin (Hydrogen)  Glucogenic amino acids form glucose
mononucleotid as needed via GLUCONEOGENESIS
e
Vitamin B3 Nicotinamide Redox Glucogenic, Ketogenic, or Both
Adenine reaction
(Niacin)
Dinucleotide (Hydride)  Glucogenic AA: the rest
(NAD+)  Ketogenic: Leucine, Lysine
Vitamin B5 Coenzyme A Carrier of acyl  Glucogenic and Ketogenic: Aromatic
group AA (F,Y,W), Isoleucine
(Pantothenic
acid)
Anabolism of amino acids
Vitamin B6 Pyridoxal Transfer of
phosphate various group  Amino acids are formed from the citric
(Pyridoxine)
to and form acid cycle intermediates
amino acids
 Non-essential Amino Acids
Vitamin B9 Tetrahydrofola Carrier of (synthesized in the body): Ex. Tyrosine
te one-carbon
(Folic acid)
unit (e.g.
 Essential Amino Acids (obtained from
Formyl group) exogenous sources such as diet):
Vitamin B12 Methylcobalam Intramolecula
(Phenylalanine, Valine, Threonine),
in/ r (Tryptophan, Isoleucine, Methionine),
(Cobalamin)
Deoxyadenosyl arrangement (Histidine, Arginine*, Lysine, Leucine)
-cobalamin *semi-essential
Amino Acid Disorders
Major classes of Enzymes
Disease Amino acid Notes
Oxidoreductases Involved in Redox involvement
reaction Phenylketonur F F hydroxylase Y↓
Ex. Dehydrogenase, ia → Phenylalanine
oxidases, peroxidases (PKU = most hydroxylase
common
Transferases Transfer of functional clinically
groups (PO4, NH2) inborn error of
AA
Ex. Kinase,
metabolism)
transaminase
Black Urine F, Y (more ↓
Hydrolases Responsible in Disease important) Homogentisat
hydrolysis (Alkaptonuria) e 1,2-
(deposition of dioxygenase
Ex. Esterases, Lipases,
homogentisic
amylases
acid)
Lyases Functional group Infantile Y (important ↓ thyroxine =
removal cretinism precursor in Hypothyroidis
synthesis of m
Ex. Decarboxylase,
thyroid
Deaminases
hormone)
Ligases Coupling Albinism Y (could not ↓ production
be converted in melanin
Ex. DNA ligase, to melanin) (white)
Isomerases Isomerization Maple syrup Problems with ↓ α-keto-acid
urine disease branched dehydrogenas
Ex. Isomerase chain amino e
enzyme, mutase acids
(L, I, V)
Hartnup Problem with ↓ neutral
Catabolism of Amino Acids disease neutral amino amino acid
acids transport
 Amino group removal: Transamination (W)
(Deamination)
 The C skeleton is broken down to:
 Acetyl CoA (ketogenic amino acids)
 Citric cycle intermediates
(glucogenic amino acids) – oxidized
to CO2 and H2O for energy

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Nucleotide = Nitrogenous base +
Sugar + Phosphate
 Bond: Phosphodiester bond
Phosphate

Nitrogenous
base

Sugar
Nucleotide
Alkaptonuria manifestation = ear is
somewhat color black Structural Organization
Primary
Thyroxine was not synthesized =
 Base or nucleotide sequence
Infantile cretinism
 Phosphodiester bonds
If patient has PKU, phenylalanine cannot
be given. Instruct the patient not to eat
Phenylalanine rich foods, instead use
Tyrosine (non-essential; essential to
patients having PKU) rich foods.
Protein Digestion
 Start: stomach
 End: small intestine
 Enzyme peptidases (proteases)
Qualitative Tests (Proteins)
Test Amino acid Result
Secondary
Ninhydrin test Amino group Rubemann’s  Helical structure
blue  H-bonds
Biuret Peptide Violet
(general test)
Xanthoprotein Aromatic Yellow-orange
amino acids
(F,Y,W)
Millon-Nasse Phenol (Y) Old rose
Hopkins-Cole W Purple
(detection of
indole ring)
Bromine Purple
water
Pauly Diazo His, Tyr Red
Lead acetate Sulfur (M, C) Black (PbS)
Sakaguchi Arginine Orange-red
Shiff Lysine Pink
*imino = Proline = yellow

NUCLEIC ACID
 Building blocks: Nucleotides Base
 Components Purine: Guanine, Adenine
1. Nitrogenous base Pyrimidine: Cytosine, Uracil, Thymine
2. Sugar (Ribose, Deoxyribose) Pairs (in DNA)
3. Phosphate Adenine = Thymine (2 H bonds)
Nucleoside = Nitrogenous base + Cytosine = Guanine (3 H bonds)
Sugar Pairs (in RNA)
Adenine = Uracil (2 H bonds)
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Cytosine = Guanine (3 H bonds)
Comparison of Types of Nucleic
Acids
Nucleic Acid DNA RNA
Number of Double Single
strands stranded stranded
Pentose deoxyribose Ribose
Purine A,G A,G
Pyrimidine C,T C,U
Cell Location Mostly Cytoplasm
nucleus Key Enzymes
 Helicases – unzipping enzyme
DNA Forms  Primases – make “primer” (to know
where to start to work)
Paramet B-DNA A-DNA Z-DNA
er  DNA polymerase – act as builder, build
Strand antiparall antiparall Antiparall new strand of DNA
el el el  Ligase – gluer or joiner
Type of Right Right Left-
Helix handed
Base pair 10 11 12
per turn
B-DNA = most abundant form
A-DNA = dehydrated B-DNA

Central Dogma of Molecular Biology


 Replication
DNA → DNA
 Production of new DNA
 Duplication 1 Helicase Unwinding the double
 Identical copies of DNA helix (by disrupting H
bonds)
Follows Principle of Semi-
2 DNA gyrase Relieves any form of
conservative replication and Anti- tension that is produced
parallelism after DNA unwinding
Anti-parallel (3’ → 5’; 5’ → 3’) 3 SSBP (single Prevents the separated
strand binding strands of DNA from
Semi-conservative replication – divide protein annealing
into 2 strands, the original strand will 4 RNA primer Composed of multiple
be used to synthesize new strands of bases that attached to
DNA; most accepted hypothesis. the template strand to
initiate DNA replication
Conservative – the whole DNA is (initates new
being replicated complementary strand
Dispersive – divided into parts and to be built)
5 Primase Build RNA primers and
linked together assembles them at the
origin of replication site
6 DNA  Creates
polymerase III complementary
(builder) strands of DNA
(5’→3’)
 Attaches to an RNA
primer
 Reads sequence in
3’→5’
 Adds nucleotides
from 5’→3’
7 DNA Removes RNA primer
polymerase I and replaces them with
the appropriate DNA
Antiparallel nucleotides
8 Okazaki Short, discontinuous
fragments stretches of DNA made
on the lagging strand
during replication
9 DNA ligase Joins DNA fragments (by
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phosphodiester bond) message physical specific
Leading strand – continuous strand carrier make up amino
of acid to
ribosom the
es ribosme
%total RNA 5% 80% 15%
cell
 Translation
RNA → protein
 Protein synthesis from mRNA
(1) Activation
(2) Initiation: ribosomal subunit attaches
to the mRNA at the initiation; start
(1) Helicase unwinds double stranded DNA codon: AUG (Met)
(2) SSBPs stabilize unwound DNA (prevent (3) Elongation: creates amino acid
annealing) sequence in order to become
(3) Leading strand is formed continuously polypeptide
(5’→3’)  Catalysis of bond at site P with the
(4) Lagging strand is formed discontinuously help of dipeptidylpeptidase
 RNA primer  translocation
 Gaps are fill out by DNA
(4) Termination: stop the process using
polymerase I
stop codons (UAG, UGA, UAA)
(5) DNA ligase joins the Okazaki fragment
Major Events in Replication
(Prokaryotes)
1. Helicases unwind the DNA double
helix
2. Primase creates a temporary RNA
primer
3. DNA polymerase (III) at the
replication fork synthesizes DNA in  Start codon: AUG
a 5’→3’ direction  Stop codon: UAG, UGA, UAA
 Leading strand (continuous) Genetic code Table
 Lagging strand
(discontinuous): Okazaki
fragment
4. DNA polymerase (I) then removes
the RNA primer and fills the gaps
between the Okazaki fragments
(short stretches of discontinuous
DNA)
5. DNA ligase then joins DNA
fragments of the lagging strand,
creating a single DNA molecule
 The newly synthesized DNA is further Mutation
modified by TOPOISOMERASES (remove  Involves a change in the shape,
supercoils in helix) structure, and nucleotide sequence
 Semiconservative replication
(1)Point mutation
 Transcription
Transitional mutation
DNA → RNA
Purine → Purine
 Controlled by the enzyme RNA
Pyrimidine → Pyrimidine
polymerase (controller and
Transversional mutation
modifier)
Purine → Pyrimidines
 Human (80s): 60S and 40S
Pyrimidines → Purines
 Bacteria (70S): 50S and 30S
Ex. UCA → UCU (Transversional
(target of aminoglycoside)
mutation)
 Creates 3 basic types of RNA
 Sickle cell anemia
Comparison mRNA rRNA tRNA  Biconcave RBCs → crescent
Description Genetic Provides Brings shape
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 Decreased oxygen transport RNA → DNA
 Enlarged spleen
VITAMINS
 Essential nutrients that our body
needs to sustain life
 Fat soluble vitamins (A,D,E,K)
VITAMIN FUNCTION DEFICIENCY
STATES
 Results of Point mutation A (retinol) - Visual - Nyctalopia
(Beta- pigment (night
 Silent mutation carotene - Anti-oxidant blindness)
 Change in codon, mutation (pro-vitamin): (beta- - Xerophthalm
occurs but the outcome is precursor) carotene) ia (dryness
same amino acid of
conjunctiva)
 Missense mutation D2 - Ca balance - Ricketts
 Different amino acid produced (ergocalciferol - Osteomala
 Nonsense mutation ) cia
D3
 Facilitate stop codon (colecalciferol
 Silent, Missense, or Nonsense? )
 UCA to UCU (Ser to Ser): Silent E (alpha- - Anti-oxidant - Neurologic
 UUU to UUG (Phe to Leu): tocopherol) dysfunction
s (rare)
Missense - RBC facility
 UAC to UAG: Nonsense K1 - Blood - Hemorrhag
(2)Frameshift mutation (Insertion, (phylloquinon clotting e
e)
Deletion) K2
Insertion or Deletion mutations (menaquinon
 A major alteration in the e)
sequence of polymerized amino K33
(menadione)
acids → altered reading frame in K4 (menadiol)
the mRNA  Water-soluble vitamins (B & C)
VITAMIN FUNCTION DEFICIENCY
STATES
B1 - Coenzyme in - Beri-beri
(thiamine) pyruvate and - Wernicke-
α- Korsakoff
ketoglutarate, syndrome
dehydrogenati (nystagmus,
on, and ataxia,
transketolase confusion)
B2 - Coenzyme in - Cheilosis
Nucleic Acid Metabolism (riboflavin) redox and
reactions seborrheic
Gout ↑ uric acid - FAD dermatitis
Deposit of monosodium B3 (niacin, - Coenzyme in - Pellagra
urate crystals, deposit in the nicotinami redox
joints which causes de, reactions
formation of tophi nicotinic - NAD and NADP
Kidney acid)
Lesch-Nyhan Decreased Hyperuricemi B5 - Functional part - Burning
syndrome HGPRT a (Panthoten of CoA Foot
(self- ic acid) Syndrome
mutilation) B6 - Coenzyme in - Peripheral
Xeroderma Deficiency of Sunburn, (Pyridoxine transaminatio neuritis
pigmentosu DNA repair freckles, dry, ) n
m mechanisms scaly skin B9 (Folic - Transfer of 1C - Megaloblast
HGPRT = hypoxanthineguaninephosphoribosyl acid) fragments ic anemia
transferase B12 - Transfer of 1C - Pernicious
(3)Spontaneous mutation = natural (Cyano- fragments anemia
cobalamin) - Metabolism of (Megaloblas
error Folic acid tic anemia
Reverse transcription (see in viruses, e.g. + spinal
HIV) cord
degeneratio
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n)
Vitamin H - Coenzyme in - Impaired fat
(Biotin) the and CHO
also called carboxylation metabolism
as Vit. B7 reactions in - Dermatitis
gluconeogenes
is and FA
synthesis
B17 (laetrile)
B15 (Pangamic acid)
C (Ascorbic - Coenzyme in - Scurvy
acid) hydroxylation (impaired
of proline and wound
lysine in healing,
collagen loss of
synthesis dental
- Anti-oxidant cement, SQ
- Enhances Fe hemorrhage
absorption )

- END -

PORLANTE, Jefferson “Tino” Aguado

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