MODULE 2

BIOCHEMISTRY
 Biochemistry
 Study of the chemical substances found in living organisms & the chemical
interactions of these substances with each other.

 Biochemical substance - a chemical substance found within a living organism.

➢ Biochemical substances are divided into two groups:
 Bioinorganic (macromolecules) = substances include H2O & inorganic salt.
o The bioinorganic substance water constitutes more than ⅔ of the mass of the
human body, + another 4%-5% of body mass comes from inorganic salts
 Bioorganic substances = include proteins, lipids, carbohydrates, & nucleic acids
o They make-up only about ¼ of the total body mass.

Cell and its Organelles

● Cell → tissues → organs → organ system → organism
 Cell is the basic structural unit of life
 Cells are of two types:
1) Prokaryotic (before nucleus) (30s=Small & 50s=Large)
 Have no nucleus & Found only in BACTERIA
 The DNA that governs the reproduction of prokaryotic cells is usually a single
circular molecule found near the center of the cell in a region called NUCLEOID
 False nuclear region.
 Prokaryotes don't have nucleus Organelles
2) Eukaryotic (true nucleus) (40s=Small & 60s=Large)
 (+) Membrane bound organelles
 A cell in which the DNA is found in a Membrane-enclosed NUCLEUS
 Cells of this type are found in all higher organisms, are about 1000 TIMES
LARGER than bacterial cells.
 Found in ANIMALS, PLANTS HUMANS
 Organelles
 “membrane-bound” structures. They have the property of “compartmentalization,”
(Nucleolus-related processes are separated/specific only to the cell part mentioned).
 Compartmentalization = regulation of DNA replication & synthesis of mRNA
 Exception:
● Ribosomes ● Cell membrane ● Cytosol
● Cytoskeleton Cytosol - fluid part of the cytoplasm Microtubules
Cell Parts FUNCTIONS
Plasma membrane/  Outer boundary of cells that controls entry & exit of substances
Cell membrane  Protection, attaches to other cells/intracellular molecules
 Part of intercellular communication & identification
 Catalyzes chemical reactions
2.) CYTOPLASM
Cytosol  Contains enzymes that catalyze the synthesis & breakdown of
molecules
 CYTOSKELETON
a) Microtubules  Support the cytoplasm & form centrioles, spindle fibers, cilia &
flagella
b) Actin Filaments  Provide structural support to cells, support microvilli (found in
small intestine→absorption)
 Responsible for cell movements
c) Intermediate  Provide structural support to cells
Filaments
 CYTOPLASMIC INCLUSION (Depend on Molecules)
i. Lipids,  Energy storage
Glycogen
ii. Hemoglobin  Oxygen transport
iii. Melanin  Skin color, ↑ melanin causes darker skin
3.) NUCLEUS
a) Nuclear  Cover nucleus, separates nucleus from cytoplasm
envelope  Allows movement of materials in/out of the molecules
b) Chromatin  DNA regulates protein synthesis (produces from process of
Translation), eg. Enzyme
 Enzyme = Chemical reaction of the cell occurs
 DNA = Genetic or Hereditary material
c) Nucleolus  Assembly site of large & small ribosomal subunits (30,40,50,60s)
4.) CYTOPLASMIC ORGANELLES
a) Ribosomes  Site of Translation/ Protein synthesis
b) Rough ER  Transportation of protein to Golgi apparatus
c) Smooth ER  Site of Lipogenesis, manufactures lipids & Carbohydrates
 Detoxifies harmful chemical & STORE CALCIUM
d) Golgi apparatus  Modifies proteins & lipids→ Packages them into vesicles for
Distribution (example: Internal use, Secretions, to become part of
Plasma/Cell membrane)
e) Secretory  Carries proteins to cell surface for secretions
vesicle
f) Lysosome  Lys = Breakdown; & contains digestive enzymes
g) Peroxisome  One site of lipid & amino acid degradation
 Breakdowns Hydrogen peroxide = HARMFUL
h) Proteasome  Breakdown of proteins in the cytoplasm
i) Mitochondria  Major site of ATP synthesis & Powerhouse of cell
 FA: Carnitine Inner mitochondrial membrane, CoA = Outer part
j) Centrioles  Centers for microtubule formation
 Determine cell polarity during cell division
k) Spindle fibers  Assist separation of chromosome during cell division
l) Cilia  Inside NOSE, Hair-like structures
 Move materials over the surface of cells
m) Flagellum  In humans, responsible for movement of SPERM CELL
n) Microvilli  Found in small intestine
 ↑ Inc. surface area for cell membrane for Absorption & Secretion

ORGANELLE PROKARYOTES EUKARYOTES

Nucleus  No definite nucleus (+) PRESENT
 DNA present but not separate from
the rest of the cell
 Concentrated in nuclear region
(NUCLEOID)
Cell membrane (+) PRESENT (+) PRESENT
(Plasma membrane)
Mitochondria (-) NONE (+) PRESENT
Endoplasmic reticulum (-) NONE (+) PRESENT
Ribosomes (+) PRESENT (+) PRESENT
Chloroplasts (-) NONE, Photosynthesisis (+) PRESENT
(if present = localized in In green plants
Chromatophores for [Link].)
Archea & Bacteria Protist, Fungi, Yeast,
Plants, Humans, Animals
 CELL CYCLE

● Duplication and division

● Highly ordered & tightly regulated
 If unregulated, will lead to abnormal development (e.g. cancers)
● Composed of 4 phases: G1, S, G2, & Mitotic phase/ Cell division/ Mitosis
● Interphase: G1, S (DNA Replication), G2
● Cell division/ Mitotic phase/ Mitosis: Prophase ➢ Metaphase ➢ Anaphase ➢ Telophase
● Note:
 Nerve cells, skin cells, etc undergo renewal
 Cell cycle is responsible for this as well as growth
 4 Main step in MITOSIS/ CELL DIVISION

PMAT/ Pro → Meta → Ana → Telo

Prophase → Metaphase → Anaphase → Telophase
1.) Prophase  Replicated chromosomes condense outside the nucleus, (segregation &
darkening) each with 2 sister chromatids.
 The mitotic spindle assembles between 2 centrosomes
● Prometaphase = Nuclear envelope breaks down allowing the
chromosomes to attach to the spindle microtubules
2.) Metaphase  Chromosomes are firmly attached to the mitotic spindle/ opposite poles
 Align at the cell’s equator but have not yet split
3.) Anaphase  Paired chromatids separate to form pairs of 2 daughter chromosomes
 Each is pulled slowly towards the spindle pose it is attached to.
4.) Telophase  Final stage where the 2 sets of separated chromosomes arrive at the
spindles.
 Chromosomes condense & become enclosed by new nuclear envelopes
 A new nuclear envelope forms around each set of chromosomes which
forms the 2 nuclei

AMINO ACIDS & PROTEINS

 Amino acids
 Building blocks of proteins
 An amino acid is an organism compound that contains both amino (-NH2) group & a
carboxyl (-COOH) group.
 The amino acids found in proteins are always α-amino acids.
α -amino acid = an amino acid 1° amine in which the amino group & the carboxyl
group are attached to the α-carbon atom. ➔ Except = Proline, an α-imino acid (2°
amine)
  Properties of Amino Acids:
1. Chirality
 Isomers have same chemical structures but different attachment/ configurations
 Carbon atoms having different 4 substituents attached
 Because of this, amino acids can exist as enantiomers
Enantiomers = (mirror images; non-superimposable; left and right-handed forms)
 The L-isomer = preferred form for amino acids
➢ Note: for monosaccharides (sugars), the preferred form is D-isomer
2. Amphoteric
 They possess properties of both acids & bases.
 ↑Nitrogen = ↑basicity

More than 700 different naturally occurring amino acids are known,
But only 20 is standard amino acids, are normally present in proteins. - A standard
amino acid is none of the 20 α-amino acids normally found in proteins
Amino Acids are grouped according to side-chain polarity.
In this system, there are four categories:
 Nonpolar AA
 Polar Neutral AA: (0) Charge/Uncharged
 Polar Acidic AA: (-) negatively charged
 Polar Basic AA: (+) positively charged

PROTEINS/ AMINO ACIDS

NAME OF TEST REAGENT USED FOR POSITIVE
RESULT
1. Ninhydrin Ninhydrin Free amino acids Violet
2. Biuret Cupric sulfate in NaOH Peptide bonds Violet
3. Hopkin’s Cole Glyoxylic acid in sulfuric acid Indole (AA: TRYPTO) Violet ring
4. Nitroprusside Sodium nitroprusside Thiol group (AA: Cys) Red
Edman’s reagent
5. Pauly’s Diazotized sulfanilic acid Phenolic & imidazole Red
groups (AA: Tyr, His)
6. Sakaguchi 10% alpha-naphthol in Guanidine group Reddish
NaBrO /NaClO (AA: Arg) /wine
7. Millon’s Mercury in nitric acid Phenolic compounds Rose/salmon
(AA: Tyrosine)
8. Amide NaOH + heat Amidic compounds Litmus paper
(AA: Asn, Gln) R→B, Blue
9. Fohl’s Lead II acetate Sulfur compounds Brown or
(AA: Cys, Met) black ppt
10. Xanthoproteic Concent. Nitric acid Aromatic compounds Yellow
(AA: Phe, Trp, Tyr)

Phenylpyruvic acid = immediate precursor of phenylalanine

 CLASSIFICATIONS OF Amino Acids/ KEY NOTES SUMMARIZE

Essential AA
Phenylalanine/ F Tryptophan/ W Histidine/ H
Valine/ V Isoleucine/ I ARginine/ R
(obtained from diet & Never Threonine/ T Methionine/ M Leucine/ L
synthesized in human) PVT-TIM-HALL or FVT-WIM-HRLK Lysine/ K
NON-ESSENTIAL → Those who aren’t included on top
Branched Chain Essential AA → VIL = Valine, Isoleucine, Leucine
VIL side chains Valine = Isopropyl Isoleucine = Secbutyl Leucine = Isobutyl
SEMI-Essential → HR = Histidine, ARginine
Essential for Infant/ Child → Non-essential for adult = H (Histidine)
Aromatic AA → WFY = TWyptophan, Phenylalanine, TYrosine
Guanidine compound → R (Arginine) Acidic → Q (Glutamine)
Alcohol/ Phenol containing → Y (Tyrosine) Primary Alcohol → S (Serine)
Sulfur containing → CM = Cysteine, Methionine
Exclusive Ketogenic → LK = Leucine, Lysine (highest isoelectric point)
Keto & Glucogenic → FITTT = Phenylalanine, Isoleucine, Tryptophan, Threonine, Tyrosine
G = Glycine (smallest Achiral AA & stable formation of Collagen triple helix, helix breaker)
A = Alanine (smallest Chiral AA) W = Tryptophan (Largest & only single codon)
21st AA= U: Selenocysteine 22nd AA= O: Pyrolysine
 ISOELECTRIC pH
 Isoelectric pH (iPH, PI, IP)
 pH where there is the presence of equal (+) & (-) charges = NEUTRAL
 pH at which the AA exists in its Zwitter ionic form
Zwitter ion - exists in both positive & negative charge; neutral; 0 charged

EXAMPLES:
 Peptide Bond Formation
 A peptide is an unbranched chain of Amino Acids (AA)
● Peptides are further classified by the number of amino acids present in the chain
a) Dipeptide = a compound containing 2 AA
b) Tripeptide = 3 AA joined together in a chain
c) Oligopeptide = loosely used to refer to peptides with 10 to 20 AA residues
d) Polypeptides = used to refer to longer peptides (>20 AA): eg. Proteins (≥ 100 AA)
The bonds that link AA together in a peptide chain are called Peptide bonds.
Number of peptide bonds = # of AA minus 1
Condensation/ Dehydration = Reaction involved in Peptide bond formation

Properties of Peptide bonds

● Has partial C=N character
(due to lone pair delocalization)

● Inherits all properties of sp2

systems, including planarity and
rigidity

● Planar - area around double

bonds are FLAT, giving definite
shape to the peptide chain

● Rigid - some parts not easily

rotated
 LEVELS OF PROTEIN STRUCTURE

Summarize: BONDS
1.) Primary  amino acids sequence in polypeptide chains  Peptide bonds
Protein structure  < 100 amino acids from Ribosomes &
Rough ER
 Least likely affected by pH
2.) Secondary  Local folding of the poly peptides chain into  (+) Hydrogen
Protein structure helices or sheets, Linear & spatial arrange bonding
 Beta-pleated & Alpha-helix  Parallel & Anti-
 2-Dimentional, Peptide bond, Parallel
 (+) Hydrogen bonding = Stabilizes the
helical/ sheet-like shape of peptide
3.) Tertiary  3-Dimentional folding pattern of a protein  Disulfide bonds
Protein structure due to a side chain interactions  Hydrophobic &
 Overall/ Combine beta pleated & alpha-helix ionic interactions
 1 sub-unit/ 1 polypeptide chain only  Hydrogen bonds
4.) Quaternary  Protein consisting more than 1 Amino acid  Disulfide bonds
Protein structure chain/ multi chained protein  Hydrophobic &
 More than 2 sub-units polypeptide chain ionic interactions
 eg.:Hemoglobin  Hydrogen bonds
Beta sheet/ Beta strand = Made up of 2/more polypeptide chains
 Protein denaturation Protein hydrolysis
●Partial of complete disorganization of a ●When Protein or smaller peptide in a
proteins characteristic 3-Dimentional solution of Strong acid/ Strong base is
shape from Disruption of its 2°, 3° & Heated, the peptide bonds are Hydrolyzed/
quaternary structural interactions Breakdown
●Reaction: Done using several ●Reaction: Reverse of peptide bond
Denaturing agents formation
●The peptide bonds remain & not ●Complete hydrolysis = All peptide bonds are
destroyed by denaturation broken, ex.: Mandelonitrile + 2 glucose
●Partial hydrolysis = Some, but Not all peptide
bonds are broken, ex.: Prunasin + Glucose
●Primary structure of proteins remains ●Leads to individual Amino Acids
Converts Peptide chain → Free amino acids

SEQUENCING METHOD
1.) Edman Reagent
 Phenylisothiocyanate (PTH) reagent, cleaves the carboxyl side of N-
terminal amino acid to the C-terminal of an oligopeptide, products are N-
terminal Amino acids attached to Phenylthiohydantoin (PTH), & the
remaining peptide
 Eg.: STC + Edman Reagent → (PTH+S) + T-C
2.) Cyanogen bromide
 Cleaves the carboxyl side of methionine
 Eg.: BIOCHEMISTRY + Cyanogen bromide → BIOCHEM + ISTRY
3.) Proteinases/ Proteases/ Proteolytic enzymes
I. Exopeptidases = Cleave off terminal amino acids
a.) Amino peptidase = Cleaves off the N-terminal amino acid (pinaka una)
b.) Carboxypeptidase = Cleaves off the C-terminal amino acid
II. Endopeptidases = Cleave peptide chains from the inside
a) Trypsin =Cleave off carboxyl side of basic amino acids.
Ex: Lysine & Arginine – Cleaves a peptide with guanidine residues in it
b) Chymotrypsin = Cleave off the carboxyl side of aromatic amino acids
Examples: WFY= Tryptophan, Phenylalanine, &Tyrosine

CLASSIFICATIONS OF PROTEINS
1. By shape: FIBROUS or GLOBULAR
FIBROUS GLOBULAR
Elongated Sphere-like
One type of sec structure Multiple sec structures
Hydrophobic/ INSOLUBLE Hydrophilic/ SOLUBLE
Structural proteins Enzymes & other important plasma protein
Collagen, Keratin, Elastin, Fibrin Myoglobin, Insulin, Hemoglobin

2. By composition: By Function
 Simple = Amino acid only
 Conjugated = Amino acids w/ additional components
Classification FUNCTION OF PROTEINS
Catalytic  BEST KNOWN as Catalysts protein
Proteins  W/ role of biochemical catalyst called Enzyme that participate in almost
all metabolic reactions
Defense  IMMUNOGLOBULINS/ Antibodies
Proteins  Central to the functioning of body’s immune system
 Bind w/ foreign substance as bacteria, viruses, etc. to help combat
invasion of the body by foreign particles
Transport  Bind to particular small biomolecules & Transport them to other
proteins location in the body & release the small molecules as needed
 HEMOGLOBIN (well known) carries oxygen from lungs to other organs
 TRANSFERRIN = carries iron from liver to bone marrow
 High DL & Low DL = carries of cholesterol in blood stream
Storage  Bind & store small molecules for future use
proteins  MYOGLOBIN = Oxygen storage protein present in muscle stored,
reserve oxygen for working muscle
 FERRITIN = Iron-storage, saves iron for use in biosynthesis of blood
Transport & Storage  Albumin, Myoglobin, Hemoglobin
Messenger  STEROIDS & HORMONE (Insulin, Glucagon, sex hormone, etc.)
proteins  Protein transmit signals to coordinate biochemical process between
different cells tissues & organs
Contractile  All forms of MOVEMENT (Actin & Myosin)
proteins  Muscles are composed of filament-like contractile proteins
 Sperms can swim due to long flagella composition
Structural  COLLAGEN = component of cartilage
proteins  KERATIN = Performs structural functions, Mechanical strength/
Protective covering to hair, fingernails & some animal shells
 Stiffness & Rigidity
Transmembrane  PROTEIN CHANNELS are very selective often allowing passage of
Proteins just 1 type of molecule or ion
 Found within the cell/plasma membrane
 Functions for enter & exit of a cell
Regulatory  Bind to enzymes w/c catalytic proteins, thereby controlling their
proteins enzymatic actions either turning ON or OFF
Nutrient  Important in early stage of life from EMBRYO → INFANT
proteins  CASEIN = found in MILK to nourish & provide immunological protection
 OVALBUMIN = found in egg white → 50% protein are found in here
Buffer  Resist drastic changes in pH & maintained acid-base balance within
proteins body fluids
 HEMOGLOBIN = also Buffering role as they maintained the Acid-Base
balance within body fluids
 TRANSMEMBRANE protein = regulate the movement of ion IN & OUT
of cells ensuring correct Acidty & Alkalinity/Basicity
Fluid-Balance  ALBUMIN & GLOBULIN = helps maintain fluid balance hydration of the
proteins circulatory system
 OTHER KEY NOTES OF PROTEIN
 Carboxyl side – RIGHT, while Amino side - LEFT
COLLAGEN  Left-handed triple helix
 Distinctive peptide chains with dominant portions
of PROLINE/ Hydroxyproline & LYSINE/
Hydroxylysine
 Proline is converted into hydroxyproline by an
enzyme known as hydroxylase which is catalyzed by
Vit. C.

HEMOGLOBIN  Transports oxygen

 Tetrapyrrole – porphyrin
 Heme & Iron in the center
 HbA = normal hemoglobin
 Hbs = hemoglobin of patients w/ Sickle cell anemia
In Sickle cell anemia, Valine replaces Glutamic acid
(Glutamic acid → Valine). Cells clump because of this &
oxygen flow gets blocked
 Sickle cell is prone to blood clot

ANTI BODIES  Secreted by B-Lymphocytes/ White blood cells

 Composed of 2 Light chains & 2 Heavy chains with
constant 2 Variable regions
 Variable regions =bind to Antigens/ Foreign bodies
 Constant region= activate immunological defenses
 Typically Y-shaped
 GAMED/ AGMED
 Monomers = IgD, IgG, IgE / EDG
 Dimeric = IgA
 Pentameric = IgM

LIPOPROTEINS (Lipids + AA) ● Low-density lipoprotein/ LDL

 Bad cholesterol / Highest Cholesterol dominant
 Transports cholesterol from liver to
Peripheral tissues
● High-density lipoprotein/ HDL
 Good cholesterol
 Transports cholesterol from peripheral tissues
to Liver
● VLDL
 Rich in Triglycerides/ TAG
● Chylomicrons
 Largest Lipoproteins
 ENZYMOLOGY
Vitamin COENZYMES/ CO-FACTOR FUNCTIONS
component
B1/  Thiamine pyrophosphate (TPP) Aldehyde transfer Cell
Thiamine respiration & presence of sulfur
B5/  Coenzyme A (CoA) Aldehyde transfer cell
Pantothenic acid respiration & fatty Acid synthesis
B2/  FAD/ FMN = Flavin adenine REDOX (Transfers/ Carriers of
Riboflavin dinucleotide (FAD) or electrons & protons)
 Flavin mononucleotide (FMN)
B3/  NAD+/ NADP+ = Nicotinamide REDOX (Transfers/ Carriers of
Niacin/ adenine dinucleotide (NAD) or electrons & protons)
Nicotinic acid Nicotinamide adenine
dinucleotide phosphate (NADP)
B6/  PXP/ PLP/Pyridoxal phosphate Transamination, Deamination.
Pyridoxine Decarboxylation
B7/H/ Biotin  Biocytin Carboxylation
B9/  Tetrahydrofolate (THF) or 1-carbon transfers nucleotide
Folic acid Tetrahydrofolic acid synthesis
B12/  Cobalamin enzyme or Deoxy Methylation, fatty acid, AA metab.
Cyanocobalamin Adenosyl Cobalamin (DAC) & Alkyl grp. or 2 carbon transfer
 Necessary for absorption of Intrinsic factor Produced by stomach

 ENZYME ( Catalytic Protein) (-ase)

 a compound, usually a protein, that acts as a catalyst for a biochemical reaction
(enzyme = catalytic proteins)
 ➢ Except: Ribozymes = made up of RNA instead of AA or proteins
 1 cell/ each cell contains thousands of different enzymes
 Almost every reaction in a cell requires its own specific enzyme.
 As catalysts, enzymes are NOT CONSUMED during the reaction but merely
HELP for RAPID reaction. They are being RECYCLED
 Enzyme catalyze biochemical reactions by altering ACTIVATION ENERGY
 Most enzymes = Globular proteins
 Prosthetic group = cofactor that is firmly/tightly bound to an Apoenzyme
 Their mechanism is to reduce the activation energy (Ea) needed for a chemical
reaction to proceed. Thus, they hasten or fasten reactions
 ZYMOGENS - Sleeping enzymes (inactive) - “-ogen”
o Chymotrypsinogen → Chymotripsin
o Pepsinogen → Pepsin (Stomach enzyme, Promotes reaction → slow at neutral pH)
o Fibrinogen → Thrombin
 Ribozymes - Composed of RNA or RNA + proteins
Enzymes are specific

 Enzyme structure
● Enzymes are biologic catalysts
● Converts reactants (substrates) into products at a faster rate than original
● Must bind properly with substrates at their active site in order to properly
catalyze the reaction.
● Enzymes are often proteins (apoenzymes) that are bound to non-proteins
that activate them (cofactors)

 Parts of an enzyme/ Pre-Requisites needed of ACTIVE SITES:

1. Holoenzyme - the protein component + non protein component, whole enzyme structure
2. Apoenzyme – Protein portion component, INACTIVE
3. Cofactor - NON-Protein component; activator, in the form of METAL ION
(e.g. minerals: Al, Zinc, Iron, etc.)
4. Coenzyme – NON-Protein component, in the form of a SMALL ORGANIC molecule
(e.g. Vitamins: such Vit. B1, B2 to B12)
 INDUCED-FIT MODEL LOCK & KEY MODEL
 Much PREFER/ ACCEPTABLE model  LESS acceptable model
 Active site has a flexible shape that can  Active site has a fixed geometric
change to accept a variety of related shape, only substrate matching shape
substrate can fit into it
 Can Explain dynamic changes that  Fails to explain the dynamic changes
accompany catalysis that accompany catalysis
 Binding of a substrate to spec. part of  Enzyme & Substrate Fit Together
enzyme → INDUCES CONFORMATIONAL (like a key to a lock).
CHANGES in the active site of enzyme

MAJOR class & SUB-class of ENZYMES

MAIN CLASSES SELECTED TYPE OF REACTION
SUBCLASS
MNEMONICS: OTHLIL
Reductase Reduction of substrate
EC1 Oxidase Oxidation of Substrate
OXIDO- Dehydrogenase Introduction of double bond
REDUCTASE eg.: Ethanol → Ethanal Removal of 2 H-atoms w/ 1 accepted
(1 EC number) by co-enzyme
EC2  Transaminase Transfer of Amino group
 Kinases Transfer of a Phosphate grp.
TRANSFERASES  DNA & RNA Polymerase
EC3  Carbohydrate Hydrolysis of Glycosidic bonds in
carbohydrates
HYDROLASES  Lipases Hydrolysis of Ester lipids
 Nucleases Hydrolysis of sugar-phosphate ester
bonds in nucleic acid
 Phosphatases Hydrolysis of Phosphate-ester bond
 Proteases Hydrolysis of Amide in Proteins
 Fumarase
EC4  Hydrate Addition of H2O to a substrate
LYASES  Deaminase Removal of NH3/Amine & Formation
of NH4/Ammonia (Deamination)
 Dehydrate Removal of H2O from a substrate
 Decarboxylase (Pyruvate) Removal of CO2 from a substrate
 Racemases Conversion of D-isomers→ L-isomers
EC5 Or L-isomer→D-isomers/ vice versa
ISOMERASES  Epimerase
(Prevent DNA breakage  Mutases Transfer of Functional grp. from 1
during replication) position to another w/ same molecule
 Synthetase Formation of new bond w/ the help of
EC6 ATP in 2 substrate
LIGASES  Carboxylase Formation of new bond between CO2
(Acetyl CoA) & substrate w/ the help of ATP
ENZYME KINETICS
 FACTORS AFFECTING ENZYME KINETICS
1) Enzyme concentration  Reaction rate ↑ = Enzyme concentration ↑
 Enzyme concentration is much lower than substrate
2) Substrate concentration  Reaction rate ↑ with substrate concentration until full
saturation occurs
3) Temperature  Reaction rate ↑ w/ temperature = Denaturation & ↓ activity
 37°C = Normal
4) pH  Maximum enzyme activity is possibly only within pH range
 ↓ or ↑ pH/ Acidic or Basic pH = Denaturation & ↓ activity

ENZYME INHIBITION
 Competitive enzyme  Molecule closely resembling substrate
inhibitor  Binds to the active site & temporarily prevents substrate
from occupying it & blocking the reaction
 Non-Competitive  A molecule that bind to a site on an enzyme that is not the
enzyme inhibitor active site/ Substrate mimics the enzyme
 Normal substrate still occupies the site but the enzyme
cannot catalyze the reaction due to the inhibitors
 Irreversible enzyme  Molecule forming a covalent bond/ Irreversible bonds to
inhibitor/ a part of active site permanently preventing substrates from
Or Uncompetitive inhibition occupying it/ No longer fully functional active site

Lineweaver-Burk Plots enzyme inhibition

Vmax Km
 Competitive  Same/ No effect  Increases
 Non competitive  Decreases  Same/ No effect
 Uncompetitive  Decreases  Decreases
 CARBOHYDRATES
 Hydrates of carbon = (C x H₂O)n = C6H12O6
 Polyhydroxy aldehydes (RCHO) / Polyhydroxy Ketones (RCOR)
 Building Blocks: Monosaccharides/ Simple SUGAR linked via GLYCOSIDIC BONDS
 Carbonyl carbon: Aldose is in Carbon 1………….Ketone is in Carbon 2
 Carbohydrate classification:
A.) By Functional group:

B.) By number of Carbons

Number of carbon Aldose (RCHO) Ketose (RCOR)
3 Triose (glyceraldehyde) Triulose (dihydroxyacetone)
4 Tetrose (erythrose) Tetrulose (erythrulose)
5 Pentose (ribose) Pentulose (ribulose)
6 Hexose (glucose) Hexulose (fructose)
Aldose = ___ose Ketose = ___ulose
C.) By number of sugar units
Number of SUGAR EXAMPLES
units
1 Monosaccharides Glucose, Fructose, Galactose
2 Disaccharides  Trehalose = glu + glu (α1 → 1α) Non-Reducing
 Sucrose = glu + fru (α1 → 2b) Non-Reducing
 Maltose = glu + glu (α1 → 4) Reducing sugars
 Lactose = glu + galact (b1 → 4) Reducing sugars
 Cellobiose = glu + glu (b1 →4) Reducing sugars
3-10 Oligosaccharides Maltotriose, Dextrin
> 10 Polysaccharides Starch, Glycogen, Cellulose
 MONOSACCHARIDE can be represented via:
 Haworth projection = Commonly used for Cyclic sugar structures
 Fischer projection = Commonly used for Linear sugar structures
o Penulmitate carbon determines whethers a –D or –L molecule
o L sugars are depicted with their hydroxyl molecule on the Left
o αlpha-OH anomers of D sugars are drawn downward

STERIOISOMERISM IN CARBOHYDRATES
1) Functional Isomerism  Differ in functional groups, GLUCOSE & FRUCTOSE
2) Anomers  Differ in configuration at the anomeric carbon
 CARBOHYDRATES
3) Epimers  Differ in configuration at only one chiral carbon
4) Enantiomers  Mirror images, Non-superimposable structures
5) Diasteromers  not real mirror image, more in the structure aren’t the same
  αlpha-OH = Downwards
 beta-OH = Upward
 STRUCTURAL SUGARS
 Vertical bonds in a Fischer projection correspond to bonds directed behind the paper,
horizontal bonds correspond to bonds oriented in front
 Haworth projection is the cyclic forms of sugars best representation

MNEMONIC FOR EPIMERS

 maNNose  2 epimer of Glucose/ C2 (Mannose + Nitric acid → Mannuric Acid)
nd

 ALLose  3rd epimer of Glucose/ C3

 GALActose  4th epimer of Glucose/ C4
C2 & C4 = Epimers of glucose
D-glucose & D-mannose = belongs to EPIMERS
 The reference carbon assign D & L isomers is the most distant chiral/ penultimate
center
CARBOHYDRATES TEST
Name of test REAGENT FOR POSITIVE RESULT
 Anthrone Anthrone Carbohydrate Green color
 Molish 10% alpha- naphtol + Carbohydrate Violet ring
ethanol (General test)
 Iodine Iodine Starch Violet
o Benedict’s CuSO4 in alkaline Reducing sugars; Brick red
/basic (Na₂CO₃) Monosaccharides
o Barfoed’s CuSO4 in acidic (Barfoed’s) Brick red
medium (Acetic acid)  Mono= <5 mins
 Disach.= >15
mins
o Fehling’s CuSO4 + Na-K tartrate Brick red
Seliwanoff’s Resorcinol HCl Ketoses Pink/ Cherry red
Bial’s Orcinol in FeCl3 & HCl Pentoses . Blue-green
Phloroglucinol Phloroglucinol Red
Phenylhydrazine/ Dinitrophenylhydrazine Osazone crystals:Yellow-orange [Link]
Osazone test/ (DNP) + Na acetate Lactose – cottonball-shaped
Kowarsky test For: SUGARS Maltose – sunflower-shaped
identification Glu/Fru/Man – needle/ broomstick-shaped
Mucic acid HNO3 / Nitric acid Galactose White Insoluble
(Galactaric acid) crystals
Weak Oxidizing agent → PCC/ Pyridinium chlorochromate
Strong Oxidizing agent → Cr, KMnO₄, Chromates
Weak Reducing agent → NaBH₄
Strong Reducing agent → LAH/ LiAlH₄

GLYCOSIDIC BOND FORMATION

 Polysaccharides
● Aka: Glycans
● 2 types:
1) Homopolysaccharides
 one type of monosaccharide only
o (e.g. Glu + Glu + Glu…)

2) Heteropolysaccharides
 2 or more than one type of monosaccharide
o (e.g. Glu + Fru + Gal.)

 Homo polysaccharides examples:

Starch:
 Amylose = Unbrached/ Linear, Helical portion (α1 → 4)
 Amylopectin = branched (α1 → 4) &
o (α1 → 6) = Branched, Water soluble portion, branching every 25-30 units
Glycogen (in animals) - storage form of glucose/carbohydrates in animals
o Present in the liver & skeletal muscle
o Similar Amylopectin but extensively branched,branching every 8-12 glucose
units
CARBOHYDRATES FUNCTIONS
The primary functions of polysaccharides are to: Provide structure & Energy storage
1) Provide structure
 Cellulose = Cell wall of the plants, Linear, linked by b1→4 bonds
 Chitin = Polymer of NAG/ N-Acetyl Glucosamine b1→4 bonds
o Found in exoskeleton of insects & crustaceans
 Pectin = Homopolysaccharides, exoskeleton & middle lamella of plant cells
 Peptidoglycan = Heteropolysaccharides component of bacterial cell walls
o N-Acetyl Glucosamine (NAG) & N-Acetyl Muramic acid (NAM)NAG-NAM-NAG-NAM→
2) Store energy (e.g. starch & glycogen)
 Starch = Plant storage
 Glycogen = Animal storage

 Heteropolysaccharides
 Glycosaminoglycans/GAG (Mucopolysaccharides)
o Components of extracellular matrix (ECM)/ ground substance of connective tissue
o Composition: Amino Acids + Uronic Acids
Glycosaminoglycans/ GAG LOCATION
Hyaluronic acid  Virtreous humor, Synovial fluids
Chondroitin SO4  Cartilage, Tendons & Ligaments
Dermatan SO4  Skin
Keratin SO4  Cornea, Nails
Heparin SO4  Basement membrane of cells
Heparin  Mast cells, Liver, Lung, Skin
LIPIDS/ FATS
 Non-polar & Structurally dissimilar/ Esters of glycerol & Fatty acids
 Common feature: insoluble in water & soluble in nonpolar solvents
 eg.: Prostaglandins, Hexane, Ether, Benzene, etc.
 Classification of Lipids Based on Hydrolysis
Hydrolyzable (Saponifiable) Lipids
 Simple (storage) – Triglycerides/ TAG (Major storage form of Fatty acids)
(triacylglycerol/TAG) Waxes & Lard
 Complex (membrane) – Phospholipids & Sphingolipids
Non-hydrolyzable (Non-saponifiable) Lipids
o Sterols
o Fat-soluble vitamins (Vit. A,D,E,K₁)
o Terpenoids/ Terpenes
o Eicosanoids
Classification of LIPIDS based on FUNCTIONS
STORAGE LIPIDS
Triacyl glycerol  Glycerol (H₂C)
o 3 FA/ Fatty Acids
MEMBRANE LIPIDS
Phospholipids a) Glycerophospholipids b) Sphingolipids
(Phosphatidic =  Glycerol  Sphingosine (backbone)
parent compound) o 2 FA o 1 FA
o 1 PO₄ + Alcohol o 1 PO₄ + Choline
Glycolipids a) Sphingolipids b) Galactolipids/ Sulfolipids
 Sphingosine (backbone)  Glycerol
o 1 FA o 2 FA
o Mono/ disaccharides o Mono/ disaccharides + SO₄
Archeal Ether Lipids 1) Glycerol 2) Glycerol 3) Glycerol
o 2 Diphytanyl o PO₄
o PO₄
 ● PO₄/ Phosphate = Polar head
● Lipids/ Tail = Apolar hydrophobic chains

● Based on Chain length (# of carbons)

● Short-chain fatty acids = 2-4 carbons
● Medium-chain fatty acids = 6-12 carbons
● Long-chain fatty acids = 14-20 carbons
● Very long-chain fatty acids = > 22 carbons

FATS = have the Highest Caloric value

upon oxidation

 Based on Saturation
Saturated FA - Purely single bonds - Good stacking
 ↑IMFA = ↑MP (melting point)
 Solids at room temp (25°C)
 “Mantikang tulog”
Unsaturated FA = Presence of double bonds - Contains 1/ more double bonds
 Less stacking because of kinks
 Presence of Cis-isomer (Lipid Naturally occurring)
 ↓MP - Liquid at room temp.

Cis isomer = Lipid naturally occurring in double bonds. If separated in the double bonds,
 it is pointed in the same direction (e.g. right & right)
Trans isomer = if separated in the double bonds,
 it is pointed in different directions (e.g. right &left)
 SATURATED Fatty acids UNSaturated Fatty acids
OYCaLaMyPaStArBeLiCe PaOLLAr
Names # of Carbons Names # of Carbons & Double bonds
CaprOic acid/ 6C Undecylenic acid 11C-1∆10
Hexanoic acid
CaprYlic acid 8C Palmitoleic acid 16C-1∆9 (Mono unsaturated)
Capric acid/ 10 C Oleic acid 18C-1∆9 (Mono unsaturated)
Decanoic acid
Lauric acid 12 C Linoleic acid 18C-2∆9,12(Poly unsaturated)
(Essential) Vitamin F
Myristic acid 14 C a-Linolenic acid 18C-3∆9,12,15 (Poly Un)
(Essential) Vitamin F
Palmitic acid 16 C: Arachidonic acid 20C-4 ∆5,8,11,15 (Poly Un)
/Hexadecanoic Most Common (from phospholipase A2)
Stearic acid 18 C Timnodonic acid 20C-5∆5,8,11,14,17EPA = (Poly)
(Eicasopentanoic acid)
Arachidic acid 20 C Carvonic acid 22C-6∆4,7,10,13,16,19 DHA = (Poly)
(DocosaHexaenoic Acid)
Behemic acid 20 C Everyone ending in structure is COOH
Lignoceric acid 24 C Octandecenoic acid = Fatty acid w/ Unsaturated
Cerotic acid 26 C = ↑ C= Highest long chain fatty acid
Melting point
 ῳ: OMEGA FATTY ACIDS
# of Carbons Examples
ῳ-3/ Omega3 o Good for the heart & brain
 α-Linolenic acid
 EPA (Eicasopentanoic acid)
 DHA (DocosaHexaenoic Acid)
o Good for brain development especially in babies
ῳ-6/ Omega 6 o Excess can cause blood clots
 Linoleic acid
 Arachidonic acid
ῳ-9/ Omega 9  Oleic acid
 Elaidic acid

 Physical properties of Fatty acids

 Physical properties of FA & Lipids that contain them are largely determined by
the length & degree of Saturation of the Fatty acid carbon chain

1) Water solubility for Fatty acids is direct function of carbon chain length
 ↑carbom = ↑Non-polarity = ↑Soluble in non-polar = ↓Soluble in H₂O
 Solubility decreases = carbon chain length increases
Short-chain fatty acids (C4 to C6)
 Have a slight solubility in water, it is related to the polarity of the carboxyl present
Long-chain fatty acids (>12 Carbons/ greater)
 Essentially insoluble to water, in longer-chain Fatty acids, the Non-polar nature
of Hydrocarbon chain completely dominates solubility considerations

2) Melting point of Fatty acids are strongly influence by both carbon chain length & degree
of unsaturation (number of double bonds present)
 As Carbon length ↑increases = Melting point ↑increases
 18C FA vs 22C FA (22C = ↑ Melting point)
 Saturated FA have higher MP than Unsaturated Fatty acids w/ same number of
carbon atoms
 “The greater the degree of unsaturation, the greater the reduction in melting point”
= ↑ Degree of unsaturation = ↓ Melting point
 18:0 Fatty acid ( ↑ MP due to saturated FA) vs 18:1∆4 Fatty acid
 Summary: carbon length ↑ = Melting point ↑ = ↓ Degree of unsaturation

Other class of Lipids

1.) Phospholipids /Glycerophospholipids/ Phosphoglycerides
 Parent compound = Phosphatidic acid
 Similar in structure in TAGs but one FA replaced with phosphate
 NAME PHOSPHOLIPID + USE
Phosphatidic acid -H (no accessory grp.) Parent compound
Phosphatidylcholine Choline AKA as “Lecithin”
Major component of Cell membrane
Phosphatidylethanolamine Ethanolamine AKA as “ Cephalin”
+Phospholipid = Cephalin Minor role in blood clotting
Phosphatidylserine Serine Role of Apoptosis/ Cell death
Diphosphatidylglycerol Phosphatidyl glycerol AKA as “ Cardiolipin”
Component of mitochondrial
membrane & non-treponemal test
Phosphatidylinositol- Inositol-4,5-bisPO4 `involved in G-protein signaling
4,-5-BisPO4

2.) Sphingolipids & Glycolipids

 Parent compounds = Ceramide
 Cerebroside are composed of ceramide + monosac
 Composed of the backbone sphingoside (an Amino alcohol) bonded to a single
Fatty acids in an amide linkage
NAME PHOSPHOLIPID + USE
 Ceramide -H (no accessory grp.) Parent compound
 Sphingomyelin Phosphatidylcholine Sphingolipid in Myelin sheath
 Cerebroside Monosaccharide + Ceramide ➢ Natural glycolipids
➢ Components of Cell
 Globoside Oligosaccharide + Ceramide membrane of neural tissues
 Ganglioside Oligosaccharide + Sialic acid ➢ Found in nervous tissue
Ceramide ➢ Acidic/ Charge glycolipid

3.) Waxes
 Esters of long-chain FA with long chain (high MW) monohydric alcohol
 (C14-C16) saturated & unsaturated FA w/ long chain (C16-C30) alcohols
 Uses: Water repellent & energy storages in some animals
 Carnauba wax
 Beeswax
 Spermaceti
 Jojoba oil
 Lanolin

4.) Sterols
 Structurally contains CycloPentanoPerhydroPhenanthrene (CPPP) nucleus
 Uses: Regulates fluidity of cell membrane, precursor of bile acids & hormones
 Cholesterol = Animals
 Phygosterol = Plant
 Ergosterol = Fungi
5.) Eicosanoids = Hydrolyzable, Formed from C20:5 Poly unsaturated fats

Phospholipids → ARACHIDONIC acid (Summary)

LOX/ Lipoxygenase (COX) Cyclooxygenase
Leukotrienes causes Inflammation or Cox 1 = Good protective function for GI Tract
Bronchoconstriction → Asthma Cox 2 = Pain, Inflammation, Vasoconstrict, Clot
Zileuton = inhibits Lipoxygenase but costly Prostaglandins causes inflammatory events
Leukotriene inhibitors = ( -lukast) COX inhibitors = NSAID/ Corticosteroids
 Montelukast & Zafirlukast for  Ibuprofen, Mefenamic acid & Aspirin
Asthma Selective COX-2 inhibitors = ( -coxib)
 Celecoxib, Valdecoxib, & Rofecoxib
6.) Terpenoids/ Isoprenoids

Vitamin A (RETINOIDS)
 Beta-carotine = Pro-vitamin A
 Retinal = Active
 Retinol = Transport form, needs bile for absorption
 Retinoic acid = Cell Growth & differentiation
 Deficiency of Vitamin A leads to
 Xerophthalmia = Dry eyes
 Nyctalopia = Night-blindedness
 Geranylgeranyl pyrophosphate = Precursor of Retinol & Phytol → 20

Vitamin D3 (CHOLECALCIFEROL) = Bone integrity & Antirachitic vitamin (Vit. D)

➢ Initially Inactive, yet Activated by Liver & Kidney
 25-OH Vit. D = Calcifediol/ Calcidiol(Most abundant circulatory form by LIVER)
 1,25-diOH Vit. D = Calcitrol (Most active form by KIDNEY)
 24,25-diOH Vit.D = Calcitroic acid (Most inactive)
 Vit. D2 = Ergocalciferol
 Deficiency of Vitamin D leads to:
 Rickets = Child
 Osteomalacia = Old

Vitamin E (TOCOPHEROL)
 Tocopherol = Biologic Antioxidants = Prevent oxidation & Free radicals
 Terminates free radicals peroxidation
 Strongest Exogenous anti-oxidant, along with Vit. A, C, Zinc & selenium
 Deficiency of Vitamin E leads to:
 Not established = HUMANS
 Scaly skin, muscle wasting, sterility = Lab ANIMALS
 Vitamin K (PHYTONADIONE)
 Vitamin K1 = Phylloquinone (green leafy vegetables = Thickens blood/Clotting)
 Vitamin-K-dependent clotting factors:
 10,9,7,2 ( Factor 10, Factor 9, Factor 7, Factor 2)
 Vitamin K2 = Menaquinone (Formed by GI flora)
 Vitamin K3 = Menadione (Synthetitc/ Artificial) only Water-soluble
 Vitamin K4 = Menadiol
 Deficiency of Vitamin K₁ leads to:
 Bleeding/ Hemorrhage = Blood clotting disease
 In Neonates = Hemorrhagic disease of Newborn
LIPIDS-REACTION TEST
NAME OF TEST REAGENT FOR POSITIVE RESULT
 Acrolein Heating Glycerol Acrid/ Burnt odor
 Osmic acid Osmium tetroxide/ OsO₄ Fatty acids (rare) Black ppt.
 Kraut Potassium bismuth iodide Choline Dark-red ppt.
 Salowski Sulfuric acid / H₂SO₄ Sterol/ Cholesterol Red
 Liebermann Sulfuric acid / H₂SO₄ Sterol/ Cholesterol Emerald Green
Burchard
 .Bromine Bromine in CCl4 Disappearance of orange

NUCLEIC ACIDS
 Nucleic acids
 Biomolecules that play a role in storage & expression of genetic information
 Building Blocks = NUCLEOTIDES linked via Phosphodiester bonds
 Polymers in which repeating unit is NUCLEOTIDE
2 types:
 DNA (DeoxyriboNucleic Acid)
 RNA (RiboNucleic Acid)
BUILDING BLOCKS SUMMARY
Carbohydrates Monosaccharides
Proteins Amino acids
Lipids Fatty acids
Nucleic acids Nucleotides
*Palmitic Acid *Malonyl-CoA
Nucleotides
 Nitrogenous base/ N-base + Pentose sugar + PO₄
Nucleosides/ Nucleotides
 Nitrogenous base/ N-base + Pentose sugar
Nitrogenous Bases
PURINE Bases (2 rings) = PurGA PYRIMIDINES Bases = PyCUT
Guanine (Gua) (DNA & RNA) Cytosine (Cyt) (DNA & RNA)
 2 rings + 1 amine + double bond O  1 double bond O + 1 Amine (NH₂)
Adenine (Ade) (DNA & RNA) Uracil (Ura) found in RNA only
 2 rings + 1 amine (NH₂)  2 double bond O + 1 methyl (CH₃)
Thymine (Thy) = found in DNA only
 2 double bond O + 1 methyl (CH₃)
  Prime (‘) C = Sugars
 Normal numbering of C = Nitrogenous Base
 Nitrogenous base

 What type of nitrogenous base?

 2 rings = Purine
 What type of purine?
 Has an amine = Adenine

 Nucleoside Deoxyribose sugar  Nucleotide

=nitrogenous Base (adenine)  can be used to make = has phosphate group,
top + Sugar bottom DNA sugar, & nitrogenous base or
= Base + Sugar = Base + Sugar +
 What sugar? Phosphate
 Ribose (C2 prime has  How many phosphate?
OH) = can be used to  1 (monophosphate)
form RNA  Ex.: Adenylate
 Ex.: Cytidine
C1’of sugar/ C1 prime = Attached to the Nitrogenous base (via N-glycosidic bond)
C5’ of sugar/ C5 prime = Attached to Phosphate group (via Phosphoester bond)
Phosphoanhydride = add/ connects PO₄ + PO₄ & so on. /Monophosphate to diphosphate
O-glycosidic bond = for monosaccharides sugars only; Oxygen bridge
N-glycosidic bond=connect base + sugar Nitrogen bridge(C1 prime in illustration above)
Phosphoester bond = connects sugar + add phosphate group to nucleoside structure
Phoshodiester bond = connects nucleotide + nucleotide
 NUCLEIC ACID STRUCTURES
 Key Convention
 Nucleotide sequence in written from 5’-end → 3’-end
 eg.: 5’-Adenine-Cytosine-Guanine-Thymine-3’ / 5’-ACGT-3’

RNA: Ribonucleic acid

 Occurs in all parts of cell
 Primary function = To Synthesize protein
 Sugar = Ribose
 Bases: C,G,A,U
 Location = Nucleus & Cytoplasm
 TYPES:
1) mRNA: Messenger RNA = largest & most heterogenous
2) rRNA: Ribosomal RNA = most Abundant
3) tRNA: Transfer RNA = Smallest, Delivers AA; specific for only 1 AA
4) snRA: Small nuclear RNA = gene expression also smallest
RNA
mRNA:  “Proton-Coding RNA”
Messenger RNA  most Heterogenous RNA & Largest
 Messenger conveying & copying information from DNA to
translation as a template
 contains Methylguanosine (in eukaryotes)
rRNA:  Responsible for Translation = Formation & function of
Ribosomal RNA Ribosomes, which acts as the site for protein synthesis
 Most Abundant RNA (80% of total RNA)
Prokaryotes have 50s & 30s subunits, made up of 3 types
Eukaryotes have 60s & 40s subunits, made up of 4 types
tRNA:  Smallest RNA, compose of weird unusual 4 bases namely:
Transfer RNA Dihydrouridine, Pseudouridine, Inosine, Ribothymidine
Anticodon = a triplet of nucleotide bases in tRNA that
identifies amino acid carrier & binds to a complementary
codon in the mRNA during protein synthesis at ribosome
snRA:  Has functions for Gene expression
Small nuclear RNA  mRNA processing or rRNA processing
miRNA:  “Smallest interfering RNA”/siRNA
Micro RNA  Responsible for gene expression regulation targeting mRNA
lncRNA:  Modulation for gene expression in many different
Long non-coding RNA mechanism

Name of Test For Positive Color

Dische / Diphenylamine Deoxyribose Blue (hydroxylevulinic Aldehyde)
Ammonium molybdate Phosphate Yellow ppt.
Murexide in KOH Purines (GA) Yellow ppt. in brown sol.
Wheeler Johnson = Br Pyrimidines (CUT) Green
Wheeler Johnson = Br(OH)2 Pyrimidines (CUT) Purple
 DNA: Deoxyribonucleic Acid
 Found within cell nucleus
 Storage & transfer of genetic information
 Passed from one cell to other during cell division
 Sugar = Deoxyribose
 Bases: C,G,A,T
 Location = Nucleus & Mitochondria
B-DNA A-DNA Z-DNA
(Naturally occurring)
Hydrated (most STABLE) Dehydrated Rare (PROKARYOTES)
Right handed Right handed LEFT handed
Clock wise Clockwise COUNTER CLOCK WISE
10 base pairs/turn 11 base pairs/turn 12 base pairs/turn
Wide major groove Narrow major groove Flat major groove
Shallow narrow minor groove Shallow Broad minor groove Deep minor groove
 Denaturation = Unwinding/ separation through melting
 Renaturation = Winding/ re-annealing/ joining/ opposite of denaturation
 5’ end of one strand & the 3’ prime end of the other strand are joined in an
Antiparallel manner to form TWO/2 DNA strands

SUMMARY RNA DNA

 Sugar Moiety Ribose Deoxyribose
 Purine compounds Adenine & Guanine Adenine & Guanine
 Pyrimidine components Cytosine & Urasil Cytosine & Thymine
 Structure Single stranded Double stranded
 Chargaff’s Does not apply Applies (Chargaff)
 Stability Unstable Stable
Can be hydrolyzed by alkali Cannot be hydrolyzed by
to 2’,3’-cyclic diesters of the alkali due to the absences
mononucleotides of a 2’-hydroxyl group
 Anti parallel Anti parallel
 Complementary based pairing
 Either Left or Right handed
 Unidirectional bidirectional
 CENTRAL DOGMA/ DNA Replication @ S-Phase
 Central dogma of Molecular biology

1. Replication
→ DNA-making duplicate/ copies of DNA
→ DNA Directed & DNA Synthesis
Enzyme: DNA Polymerase

2. Transcription
→ RNA-making (mRNA) from DNA
→ DNA-directed RNA synthesis (mRNA)
Enzyme: RNA Polymerase/

3. Translation
→ Protein-making from RNA
→ RNA-directed protein synthesis
Enzyme: Ribosomes

*Reverse Transcription: RNA to DNA instead of proteins

 Reverse Transcription

1. Replication
→ DNA-making duplicate/ copies of DNA
→ DNA Directed & DNA Synthesis
Enzyme: DNA Polymerase

2. Reverse Transcription
→ RNA makes DNA
Enzyme: Reverse transcriptase

*only DNA is produced but damages the

body causing/ worsening the disease
 Retroviridae (causes HIV)
 HEPA B
*No protein production etc.
 1.) DNA REPLICATION (DNA Synthesis)
 Occurs at S-Phase
 DNA-directed DNA synthesis
 Production of DNA
 Characteristics:
 Semi-conservative
 Replication is Bidirectional: 5’ → 3’ & 3´→ 5’
 Each strand from double helix of DNA serves as template synthesis of
complementary strand
 High fidelity of replication (contains Proof-reading)
 Because of the properties of DNA polymerase enzyme

1.) REPLICATION steps

1.) Initiation a) Recognition of origin of replication (oriC) = DNA A protein
b) Unwinding of double helix = DNA Helicase
c) Stabilization of the replication fork/bubble
 Topoisomerases = Prevent coiling/curling & must be linear
 Type 1/ Swivelase → cleaves 1 strand
 Type 2/DNA Gyrase → Relieves supercoiling
 Single-stranded binding proteins = prevent winding/ re-
annealing
2.) Elongation  DNA Polymerase
 Synthesis of DNA
 Unable to initiate Polymerization & requires PRIMERS
 Primase
 RNA polymerase that synthesize RNA Primers
3.) Termination a) Removal of primers & filling of gaps = Exonuclease (DNA Poly1)
b) Joining OKAZAKI Fragments = DNA Ligase
 TOPOISOMERASE (more notes)
TOPOISOMERASE 1 TOPOISOMERASE 2
 Eukaryotes, Prokaryotes  DNA gyrase
 Inhibits by ETOPOSIDE drugs
 ATP not required  ATP required
 Nuclease, Ligase  Prokaryotes, [Link] performs actual elongation
 Cleaves 1 strand to break  Cleaves both/ double strand to break
 Relaxes Negative (-) supercoils  Relaxes Both (+) (-) supercoils

DNA POLYMERASES (Bacterial) Functions

FUNCTION 1 (I) 2 (II) 3 (III)
1. Elongation (5’ → 3’) polymerase activity   
2. Proof reading & repair (3’→ 5’ Exonuclease)   
3. Removal of primers & repair (5’ → 3’ Exonuclease) 
ENDONUCLEASE = Attainment of high degree of specifity

ADDS ON TO REMEMBER:
Helicase  Separates/ Unwinds 2 strands from the origin
Topoisomerase  Relieves strain/ supercoiling, Prevent coiling/curling
Primase  Adds RNA primers.
Ligase  Connects Okazaki fragments.
Okazaki Fragments  Discontinuous stretches in w/c lagging strand is initially
synthesized during DNA replication
Purified Rayon  Polymer commonly employed as a surgical aid
5’ → 3’ Polymerase  Elongation/ DNA synthesis (by polymerase 3)
5’ → 3’ Exonuclease  Primer removal & mutation repair (by DNA polymerase 1)
3’→ 5’ Exonuclease  Proofreading/ copying / repair (for mismatch)
DNA → RNA → Protein  Direction information flow during GENE EXPRESSION
 2.) TRANSCRIPTION (RNA Synthesis)
 DNA-directed RNA synthesis
 Product: mRNA
 Characteristic:
 Unidirectional
 RNA polymerase (enzyme) performs majority of the process
 Lower Fidelity compared to replication
 Uses 1 strand only not both strand
 Occurs for individual genes
RNA polymerase = Holoenzyme: α₂BB2ῳo
 Core unit: α₂BB2ῳ = responsible for polymerization/ elongation
 Sigma factor: o = recognition of promoter region/ origin
 Intrinsic helicase activity
 Works only in 5’ → 3’ direction
 Can polymerization Without primers
 No proof-reading ability
Mammalian RNA Polymerase (RNAP)
RNAP Product Remarks
RNA Polymerase 1 (I)  rRNA
RNA Polymerase 2 (II)  mRNA  Inhibited by α-amanitin
from Amanita phalloides
(deathcap mushroom)
RNA Polymerase 3 (III)  tRNA
No mRNA= No protein synthesis (facilitates translation)
 2.) Transcription steps
1.) Initiation  Find promoter region (through sigma polymerase)
a) Eukaryotes = TATA box/ Hogness box/ Thyrosine + Adenine
b) Prokaryotes = Pribnow
2.) Elongation
RNA TEMP. DNA  POLYMERIZATION
G C G
DNA template = Antisense strand,
C G C
Non-coding strand
U A T
DNA Non-template = Sense & Coding
A T A
strand

3.) Termination a) Rho (p) dependent = Terminated/ Present by Helicase

b) Rho (p) independent = Termination by itself/ Stop automatically

Post-Transcriptional Modification (EUKARYOTES)

a.) Capping  For protection of mRNA structure
 Addition (+) of 7-methyl guanosine cap at the 5’-end
b.) Polyadenylation  Addition (+) of Poly-A-tail at the 3’-end
c.) Splicing Introns = Removed/ spliced away due to NON-CODING portions
Exons = Combined together to CODING portions
3/ Three = Average codons for each Amino acids

Polymerase FUNCTION
Pol-alpha  DNA synthesis
Pol-beta  Repair
Pol-delta  Elongates Okazaki fragments
Pol-epsilon  Elongates the leading strand
Pol gamma  Replicates mitochondrial DNA
 GENETIC CODE
 Codon → triplet of adjacent nucleotide bases that code for a specific amino acids
 4x4x4 = 64 codons
 61 Coding
 3 Stop Codon (Non-coding)
 UAG
 UAA
 UGA
Start/ Initiation Codon → AUG
 Methionine for Eukaryote
 N-formyl Methionine for Prokaryote
 Features of Genetic Code:
1. Universal
2. Degenerate = may have more than 1 triplet coding for a given Amino acid
 Except AUG (Methionine) & UGG (Tryptophan)
3. Unambiguous/ Specific = 1 codon = 1 A.A.
4. Non overlapping & Comma less
 3 at a time, only stop with the stop Codon & start again with AUG/ Methionine
 3.) TRANSLATION (Protein synthesis)
 RNA- directed Protein synthesis
 Production of PROTEINS
 Peptidyl Transferase enzyme role → Peptide bond formation between adjacent Amino
acid
3.) TRANSLATION steps
1.) Activation of tRNA  Aminoacyl-tRNA synthetase/ AA + ATP + AMP + PPi
 Implement genetic code (specific)
 Activate amino acids for peptide bond formation
 Wobble pairing→ Less stringent/nontraditional base pairings

2.) Initiation  Formation of initiation complex

 Bind to mRNA to small ribosomal subunit
 Eukaryotes: 60s Large ribosomal sub-unit
 Eukaryotes: 40s Small “ “ “ “
 Prokaryotes: 50s Large ribosomal sub-unit
 Prokaryotes: 30s Small “ “ “ “
 Recognition of Chain initiating sequence to find the start of
Codon/ AUG
 Binding sites of Eukaryotes
 Kozak sequences/ 5’ cap = Methionine (AUG)

 Binding sites of Prokaryotes

 Shine-Dalgano sequences = N-Formylthionine (AUG)
3.) Elongation  Found in Large ribosomal unit
 E = Exit site
 P = Peptide bond formation site
 A = Attachment site
 AA + AA forming Peptides → Polypeptides → PROTEIN
4.) Termination  Release factor recognizes the Stop codon/ Nonsense codon
completed Polypeptide is release
 Hydrolysis of bonds between the peptide & tRNA
 Dissociation of Ribosome assembly
 Golgi apparatus → Packaging & transfer of Post-Translation
 PROTEIN SYNTHESIS INHIBITORS
 30s Protein synthesis Inhibitors: (small ribosomes)
 Aminoglycosides
 Tetracyclines
 50s Protein synthesis Inhibitors: (large ribosomes)
 Chloramphenicol, Macrolides, Lincosamides, Linezolid

MUTATIONS
1.) Small scale: Point Mutations
 Alteration in one base only

Transition:
 Purine ↔ Purine
 Pyrimidine ↔ Pyrimidine
 Adenine is replace by guanine
Transversion:
 Purine ↔ Pyrimidine
 Pyrimidine ↔ Purine

 Silent mutation = No Amino acid changes

 Nonsense mutation = Stop codon/ AUG
 Missense mutation = Coding of a different amino acid, Asp
 eg.: Transversion missense: Sickle cell anemia - Glutamic to Valine

2.) Large scale: Frame shift mutations

 Shifting of reading frame by:
 Duplication/ Insertion
 Deletion
DNA DAMAGE & REPAIR
 Repair of Damage cause by UV LIGHT:
 8-10 am → Optimal UV light
 7-dehydrocholesterol - vit D in the skin
Nucleotide Excision Repair/ NER
 Treatment for Recognition & excision of UV induced dimers
 Treatment for UV radiation & Cancers
 Xeroderma Pigmentosum
- Defective NER
- Accumulation of mutations & early numerous skin cancers
Polymerase Chain Reaction /PCR
 Example of DNA polymerase that Mimics Replication
1. Denaturation → 95°C w/ the help of Thermus aquaticus/ Bacteria in heat temp.
2. Annealing → 55°C Taq polymerase
3. Elongation → 72°C repeat cycle for 20-40 times

Note:
Recombinant DNA technology - Antibiotics
Pro - inactive & Xero - dry
Lipid naturally occuring isomer - Cis
Carbohydrates naturally occuring isomer - Dextro
Higher melting point = Strong forces (structured bonds)

Unit 8: METABOLIC PATHWAYS

 Metabolism
 Sum of all chemical reactions in the body (Reactions are catalyzed by specific enzyme).
 A series of metabolic steps with a specified end-product is called a Metabolic pathway

● Metabolic pathways are Linear (e.g. glycolysis) / Cyclic

● Metabolic pathways are either Catabolic / Anabolic
● Each pathway usually has an irreversible reaction to dictate the direction of process
 → (unidirectional; irreversible)
 ⇄ (bidirectional; reversible) 63

 Carbohydrates - main energy source (Carbs > Fats > Proteins)

 Anabolism = use of smaller molecules + energy to form Larger molecules
● E.g. Creating a nucleotide from a nitrogenous base
Catabolism = breakdown of large molecules to form Smaller molecules + energy (ATP)
● E.g. Hydrolyzing proteins to form amino acid
Catabolism & Anabolism, by direction, are direct opposites
METABOLIC PATHWAY Type of Metabolic Reaction
 Glycogenesis - formation of glycogen  ANABOLIC
 Gluconeogenesis - formation of new glucose  ANABOLIC
Glycolysis - breakdown of sugar/glucose CATABOLIC
Glycogenolysis - breaking down glycogen CATABOLIC
Beta-oxidation of fatty acids CATABOLIC
(Fatty acid breakdown) / LIPOLYSIS
 Glycolysis  AMPHIBOLIC (both Ana & Cata)
 Kreb’s cycle  AMPHIBOLIC (both Ana & Cata)
 Electron transport chain  AMPHIBOLIC (both Ana & Cata)
(Oxidative phosphorylation)
 Classic equation for CELL RESPIRATION:
(glucose)C₆H₁₂O₆ + (water)6O₂ → (carbon dioxide)6CO₂ + (water)6H₂O + ATP
 Reverse of the equation for cellular respiration is for plant respiration
 Cytosol
 Most common sites of metabolic reactions inside the cell.
 Fluid portion of Cytoplasm
 Mitochondrion/ Mitochondria
 Most common sites of metabolic reactions in cell.
 Powerhouse/ ATP synthesis site
 Outer membrane
 Inner membrane = causes the formation of cristae
 Matrix = Fluid portion of mitochondria

ATP/ Adenosine Triphosphate

 Primary energy currency
 Adenine = Purine
 Ribose sugar
 Triphosphate
Cofactors that equate to some ATP:
 NADH = 2.5 ATP (only become ATP after going through ETC)
 FADH₂ = 1.5 ATP (only become ATP after going through ETC)
 Respiration
 involves most biomolecules
 They converge at acetyl-CoA, which ultimately enters the citric acid cycle
 Small intestine - optimal site of absorption of food and drugs
● Duodenum - main site
● Jejunum & ileum
Once the absorbed fats, carbohydrates & proteins are absorbed into the cells in the form of
acetyl-CoA, they undergo different pathways
 Citric acid pathway - common metabolic pathway; final common pathway; central hub
 GLYCOLYSIS/ Carbohydrate Metabolism
 Aka Embden-Meyerhof-Parnas Pathway
 Breakdown of glucose (6 carbons) to 2 molecules of pyruvate (3 carbons)
 Cytosolic & Generally energy producing
Consists of 2 phases:
a) Energy investment/spending/expenditure - Steps 1 & 3 ➔ use ATP
b) Energy payoff/producing/generation - Steps 7 & 10 ➔ produce ATP
Reactions: PIPCIOSIDS (10steps/reactions)
Enzymes: HPPATGPPEP (10 enzymes)
Location: CYTOSOL
Start: Glucose & End: Pyruvate
10 Steps: PIPCIOSIDS 10 Enzymes: HPPATGPPEP
1) Phosphorylation = Energy spending (-1) 1) Hexokinase = 1st Irreversible step
2) Isomerization 2) Phosphoglucose isomerase
3) Phosphorylation,Energy spending (-1) 3) Phosphofructokinase, 2nd Irreversible
4) Cleavage 4) Aldose
5) Isomerization 5) Triosephosphate isomerase
6) Oxidative phosphorylation 6) Glyceraldehyde 3-P dehydrogenase
(only oxidative step) (For pre-Kreb cycle, NADH product)
7) Substrate level phosphorylation = 7) Phosphoglycerate kinase (1st substrate
Energy producing (+2 ATP) level phosphorylation in glycolysis)
8) Isomerization 8) Phosphoglycerate mutase
9) Dehydration 9) Enolase
10) Substrate level phosphorylation = 10) Pyruvate kinase = 3rd Irreversible
Energy producing (+2 ATP) (2nd substrate level ) (K/ Potassium = acts
as prostethic group of Pyruvate Kinase)
ATP yield
 Losses at step 1 & 3
 Gains at step 7 & 10
 Total = 10 ATPs
NADH yield
 Gain at Step 6 = TOTAL → 2 NADH
Irreversible steps enzyme:
 Single-headed arrows = Steps 1-HK, 3-PFK & 10-PK
 STEPS: 1-HexoKinase, 3- PhosphoFructoKinase, 10- Pyruvate Kinase
First ATP-producing step @7: 1,3-bisphosphoglycerate → 3-Phosphoglycerate
 Kreb’s Cycle/ CITRIC Acid cycle/ TCA
 Cycle that converts acetyl-CoA (2) → 2 molecules of CO₂
 The “CENTRAL HUB”
 The “FINAL COMMON PATHWAY”
 Location: MITOCHONDRIAL MATRIX
 Amphibolic
 Citrate = Fatty acid synthesis
 α-kg = Amino acid Catabolism
 Succinyl-CoA = Heme synthesis
 OAA/ Oxalo Acetate = Gluconeogenesis & nucleotide synthesis
Product from Acetyl = 2
 1 cycle = 10 ATP
 Other cycle = 10 ATP
 Total = 20 ATP
 FADH₂ = Produce from Succinate → Fumarate
 Succinyl-CoA synthetase =enzyme that catalyzes substrate level of phosphorylation step
 For every acetyl CoA = energy unit (NADH, GTP, FADH2 = ATP)
 Step 3,4,8 = NADH
 Step 5 = GTP
 Step 6 = FADH₂
 Non-energy production = Citrate → Isocitrate
 Note: 1 complete cycle of TCA cycle = 2 CO₂ & 3 NADH are formed
 Rate Limiting Step: Isocitrate dehydrogenase
 Majority from the CO₂ that We exhale comes from Krebs cycle

Electron Transport Chain/ ETC/ Oxidative phosphorylation

“Oxidative phosphorylation” Because ETC involved electrons & protons
Concentration = regulation of Phosphorylation & glycosylation
Antimycin A = Inhibits (-) Cytochrome reductase
➢ Oxidation & Reduction reactions
 Location: INNER MITOCHONDRIAL MEMBRANE
 Consists of 4 main complexes that are coupled to ATP synthase (enzyme) NSUCCA
➢ Complex I: NADH-CoQ reductase, NADH enters
➢ Complex II: Succinate-CoQ reductase, FADH enters
➢ Complex III: Ubiquinone/ CoQ-cytochrome c reductase
➢ Complex IV: Cytochrome c oxidase, Cherry red blood Oxygen last e- acceptor
➢ Complex V: ATP synthase
When is ETC activated?
 ETC works only when ATP levels are low, & Produces ATP as a response
When is ETC deactivated/slowed down?
 ETC will slow down when ATP levels are high
 ➢NADH was able to generate 10 protons
(hydrogen) by passing through complex I-V
➢NADH was able to generate 6 protons
(hydrogen) by passing through complex II-V

➢Note: Hydrogen in complex V = Not

counted since its already inside the matrix

Computation involving ETC

 NADH Shuttle mechanism
 Important for NADH produced from gglycolysis
1) Malate-Aspartate shuttle (MA shuttle)
 Used by Liver & Heart muscles/tissues
 More energy produced(produces 2.5 ATP per NADH)
 Passes through Complex I (1) → Complex V (5)
 Generated 10 H+ & Reduces Oxaloacetate

2) Glycerol-3-Phosphate shuttle (G3P shuttle)

 Used by Skeletal muscles & Brain tissues
 Less energy efficient (produces 1.5 ATP per NADPH)
 Passes through Complex II (2) → Complex V (5)
 Generated 6 H+ & Reduces Dihydroxyacetone phosphate
 Pre-krebs & Krebs cycle doesn’t need a shuttle = Coz it is matrix → Near the inner
mitochondrial membrane (Only NADH from glycolysis needs shuttle)
Liver & heart don’t rest = needs more energy
Brain & muscles rest = needs less energy

Aerobic Glycolysis ATP YIELD

 Anaerobic Glycolysis ATP YIELD

● Anaerobic = no kreb’s cycle need

(no production of acetyl coA which is
produced in pre-krebs cyle) since
pre-krebs cycle or fate #1 is aerobic
or uses oxygen

GLUCONEOGENESIS/ GNG/ Glucose synthesis

 Formation/creation of new glucose
 Metabolic pathway by which glucose is synthesized from non-carbohydrate materials.
● Non-carbohydrate starting materials/ Substrate are:
1. Pyruvate (from glycolysis)
➢ Pyruvate → Pyruvate decarboxylase → Acetaldehyde
➢ Pyruvate → Pyruvate Carboxylase →↑ levels of Acetyl-CoA can enhance rate of GNG
 Glucose to pyruvate: Glycolysis
 Pyruvate to glucose: Gluconeogenesis
2. Lactate (from hardworking muscles & from red blood cells)
 Through Cori cycle
 Also a product of anaerobic metabolism
3. Glycerol (from triacylglycerol hydrolysis)
 Breakdown of glycerol backbone & FA linkage
4. Certain amino acids (from dietary protein hydrolysis/ From muscle starvation)
 Which are glucogenic amino acids only
Gluconeogenesis/ hydrolysis of Glucose-6-phosphate: 90% in liver & 10% in kidneys
Function: Gluconeogenesis helps to maintain normal blood-glucose levels in times
of inadequate dietary carbohydrate intake (such as between meals)
Note: Gluconeogenesis is
reverse of glycolysis (Steps
1, 3, & 10 are irreversible),
thus, the corresponding steps
in Gluconeogenesis take
place since they’re
reversible steps
 Cori cycle/ GNG of cyclic lactate
 Type of Gluconeogenesis w/c recycles
Lactate/ Lactic acid
 LACTATE = Gluconeogenesis precursor
obtained from cori cycle
 Glucose is converted to lactate in muscle tissue
 Lactate is converted/recycled to glucose in liver
 Lactate is converted/recycled to pyruvate in liver
 Glucose is brought/return by blood to muscle
 Lactate dehydrogenase = process that supplies
the NAD needed by Glycolysis/ G3-phosphate

 Glycogen = storage form of glucose in animals

 ↑Glucose = store excess in glycogen
 ↓Glucose/Fasting = pyruvate to glucose via gluconeogenesis / Stored glycogen
breakdown to form glucose
 Deficient of Gluconeogenesis = Von Glerke’s disease → Hypoglycemia
GLYCOGEN Metabolism
 GLYCOGENESIS GLYCOGENOLYSIS
 Stimulated by insulin since they have  Glycogenolysis breaks down
similar goal glycogen
 For lowering glucose level  Stores glucose/ ↑ blood Glucose level
 SYNTHESIS of glycogen from glucose  BREAKDOWN of glycogen to glucose
 Glucose-6-phosphate → Glycogen  Glycogen → Glucose-6-phoshate
 Glucose-6 PO4 (substrate) → Glycogen
 ANABOLIC/ Formation  CATABOLIC/ Breakdown
 Requires FORMATION  Requires HYDROLYSIS
of a1,4 & a1,6 bonds of a1,4 & a1,6 bonds
 Stimulated by: INSULIN  Stimulated by: GLUCAGON
 Effect: ↓ Reduced blood sugar  Effect: ↑ Increased blood sugar
 Timing: Fed State  Timing: Fasted state
 Key enzymes: UDP-glucose  Key enzymes: Glycogen phosphorylase
pyrophosphorylase & glycogen synthase → Breakdown of a1,4 bonds & a1,6 bonds
→ Formation of a1,4 & a1,6 bonds (Rate limiting step of Glycogenolysis)

GLYCOGEN STORAGE DISEASES

 Diseases in the metabolism of glycogen
 Commonly lead to hypoglycemia, hyperlipidemia, & hepatomegaly & some are fatal
Glycogen Storage Disease Type Enzyme Defficient
GSD type (Common Name)
Type 0 Zero Glycogen synthase
Type 1 Von gierke G-6-Phosphatase
Type 2 Pompe Lysosomal alpha-glucosidase
Type 3 Cori Debranching enzyme
Type 4 Andersen Branching enzyme
Type 5 McArdle’s Muscle phosphorylase/ Glycogen
Type 6 Hers’ Liver phosphorylase/ Hepatic
Type 7 Tarui’s PFK
Mnemonics: Very Poor CArbohydrate Metabolism in Her Tammy

Pentose Phosphate Pathway/ Hexose Monophosphate Shunt/ HMP Shunt

 AKA: Hexose Monophosphate Shunt (HMP Shunt)
FUNCTIONS:
● Produces NADPH
● Produce Ribose-5-Phosphate required for
biosynthesis of nucleotides
● Provides a mechanism for metabolic use of
5-carbon sugars
● PPP = Main source of reducing equivalents NADPH
for lipogenesis
 PPP doesn’t produces nor consumes ATP

Location: CYTOSOL
NADPH & NADH = NOT the same
 NADPH/ Nicotinamide Adenine Dinucleotide Phosphate NADH
 Required by CYP450 mono oxygenase  Cofactor that can be converted
(Important for Phase 1 metabolism) into ATP units through ETC
 Creation/Synthesis of Fatty acids &  Equivalent to 2.5 ATPs
steroids
 GLUTATHIONE reduction inside RBC
- Strongest Endogenous Anti-oxidant from liver
- No NADPH = Glutathione will NOT BE ACTIVE
IV GLUTATHIONE
→ FDA approved in Phil. as adjunct treatment in Cisplatin Chemotherapy
 Oxygen-dependent bactericidal mechanism of WBCs
 Synthesis of Nitric oxide

G6PD deficiency = impaired pentose phosphate pathway; no NADPH production

PPP has 2 PHASES:
1) Phase 1 = OXIDATIVE Phase
2) Phase 2 = NON-Oxidative Phase

 Phase 1 = OXIDATIVE Phase → To control oxidative stress

 Involves 3 steps
 Produces NADPH @ step 1 & 3
 Uses of NADPH: Lipid Biosynthesis & Detoxification (via glutathione)
 Production of Ribulose-5-phosphate
 Provides endogenous antioxidant activity from Glutathione
 Participation of G6P dehydrogenase
 Ribulose → Phosphopentose epimerase(enzyme) → XYLULOSE 5-PHOSPHATE
 Phase 2 = NON-Oxidative Phase
 Leads to synthesis of other sugar phosphates
 Merely a shuffling carbons between pairs of sugars
 Can simply lead back to glycolysis or
 To lead to Ribose-5-Phosphate for nucleotide synthesis (Aid DNA Synthesis)
 Key enzymes:
 Transketolase & Trasaldolase
G6PD = a key enzyme in the conversion of NADP → NADPH (glutathione activity)
Glucose-6-phosphate dehydrogenase Deficiency/ G6PD-Deficiency
 Cells (especially RBC) are susceptible to OXIDATIVE STRESS
 When triggered by drugs/ Reactive oxygen species (ROS), causes Hemolysis (related
consequences to Jaundice & Dark urine)
 Inherited disease characterized by Hemolytic Anemia caused by inability to detoxify
Oxidizing Agent
 Most common disease-producing enzyme abnormality in humans, affecting more
than 400 million individuals world wide
 Characterized by presence of Heinz Bodies, Blister cells, Bite cells/Helmet cells in RBC
 Heinz bodies: most distinct manifestation of G6PD deficiency
Summary of Major Carbohydrate pathways
 LIPID Metabolism
FATTY ACID SYNTHESIS/ Lipogenesis
 Location/Occur: CYTOSOL
 RLS: Conversion of acetyl-CoA to Malonyl-CoA by Acetyl-CoA Carboxylase (ACC)
 When synthesized, fatty acids are esterified into phospholipids & triglycerides
 Timing: Fed-state (stimulated by insulin)

2 to 3 carbons
Start with acetyl coa → form malonyl coa → add malonyl coa until a certain chain of FA
(example illustration) is formed
Malonyl-CoA = Building block of Palmitic Acid
  Fatty acid breakdown is a catabolic process Odd numbered, long-chained, & FAs with
double bonds cannot undergo FA breakdown
 End product of every lipid breakdown/beta-oxidation = 1 Acetyl CoA
1) # of acetyl coa = number of carbons of the FAs divided by
2) # of β-oxidation = number of acetyl coa minus 1
 Example: Arachidic acid (20C saturated FA) = 10 Acetyl CoA & 9 β –oxidation

FATTY ACID BREAKDOWN

 There are 3 parts to the process by which Fatty acids are broken down to obtain energy
1) The Fatty acid must be Activated by bonding to coenzyme A
2) The Fatty acid must be Transported into mitochondrial matrix by a shuttle
mechanism
3) The FA must be Repeatedly oxidized, cycling through a series of 4 reactions to
produce acetyl CoA, FADH2 & NADH (For every cycle of lipolysis)

 Note: must be charged with ATP (ATP is spent) AMP = Adenosine monophosphate
 ATP → AMP = 2 phosphate bonds/groups are used

● Note: Acetyl CoA= principal product of the

B-Oxidative decarboxylation of Pyruvate

● 4 ATPs per β-oxidation cycle

(1 FADH2 x 1.5 & 1 NADH x 2.5)
FATE OF ACETYL Co-A
1) TCA cycle = The usual where Acetyl CoA goes during fed state
2) Ketone bodies = During prolonged starvation, this is where the excessive Acetyl-
CoA goes
o Enzyme: HMG-CoA Lyase (when deficient → causes underproduction of
Ketone Bodies)
3) Sterols & Fatty Acids = When there is a need to synthesize sterols & fatty acids,
this is where Acetyl-CoA proceeds.
o Enzyme: HMG-CoA Reductase (Rate limiting step of Cholesterol Synthesis)
o : HMG-CoA Reductase = enzyme targeted by Cholesterol lowering agents
Enzymes are saturable (excessive Acetyl coa that enters the Krebs cycle will make the
enzymes saturated/tired). This results to the formation of ketone bodies
↓carbohydrates → glycogen breakdown → if glycogen runs out → fat breakdown
(beta-oxidation) → excessive
Lipolysis/beta oxidation = A fatty acid spiral that degrades fatty acids in 2 carbon
increments as acetyl-CoA & saturated TCA cycle = excess
 More carbons → more energy expected
Acetyl coa (prolonged starvation) = continous
Acetyl coa = ketone bodies (acidic; abnormal)
 Mevalonate = Product formed during rate-limiting step of Terpenoid & steroid synthesis
 Ketones: Serves as the emergency fuel of the brain in some cases
 Brain can’t use fats due to the BBB/ Blood brain barrier,
 Tissues normally shift from using Sugars to Fats
 Ketosis = Shift from dependence on glucose to dependence on ketone bodies
 Ketonemia→ Elevated KB in Blood (20mg/100mg)
 Ketonuria→ Elevated Kb in urine (70mL/100mL)
 Ketoacidosis→ excessively elevated ketone bodies causing acidification of blood
 Ketogenic diet = induced ketosis
 ↓ No Carbohydrates, Not recommended to public
 ↑ Increase Fats/ Protein diets
DISORDER ENZYME DEFICIENCY
 Tay-Sachs disease  Hexosaminidase A
 Sandhoff’s disease  Hexosaminidase A & B
 Niemann-Pick disease  Sphingomyelinase
 Fabry’s disease  α-Galactosidase & Sphingo
 Metachromatic leukodystrophy  Arylsulfatase A & Sphingo
 Krabbe’s disease  β -Galactosidase
 Landing’s disease  β–Galactosidase
 Gaucher’s disease  β-Glucosidase
 Farbers disease  Ceramidase
 Austin’s disease  Multiple sulfatases
 Wolman’s  Acid lipase

Nucleotide & Amino Acid Metabolism

●Denovo = From scratch/ New
●Salvage = To save/ Recycling

●Parent/precursor purine = IMP/

Inosine monophosphate
*breakdown of Purines → ↑ Uric acid
*Insoluble/ can’t be urinate → destroys
goes Purine metabolism → Uric acid
*Purine breakdown/ Xanthine oxidase
*Alopurinol = (-) Xanthine (for gout)

●Parent/precursor pyrimidine = OMP/

Orotidine monophosphate
●Having these precursors allows
production of the products

● End products of Purines = Uric acid

or Urate
●Lesh-Nyhan = disease related to
salvage of Purine metabolism
● Severe combined immunodeficiency
→ absence of adenosine deaminase
SHIKIMIC ACID Pathway
 Amino Acid Products
 Tyrosine  Catecholamines = Epi, Norep, Dopa, L-dopa
 Thyroid hormones = T₃ & T₄
 Melanin = skin pigment
 Tryptophan  Serotonin
 Melatonin = Sleeping hormone
 Niacin
 Histidine  Histamine
 Serine  Choline/Lecithin
 Glutamate  GABA = Inhibits Neurotransmitters
 Glycine a-helical secondary protein & Heme = Structure of Hemoglobin
 Aginine  Nitric oxide = Vasodilator
 Common Inborn errors of Metabolism (IEM)/ AMINO ACIDOPATHIES
Name Amino Acid AFFECTED Enzyme Deficient
 Alkaptonuria/  Tyrosine  Homogentista oxidase
Black urine disease  1st discovered Aminoacidopathy
 Albinism/ Vitiligo  Tyrosine  Tyrosinase
 Synthesizes Melanin from Tyrosine
 Homocystinuria  Methionine  Cystathionine synthetase
 Phyenyl Ketonuria  Phenylalanine  Phenylalanine hydroxylase
(PKU)  Aspartate (child)  Rare inherited disorder
 Maple syrup urine  Branched-chain  Branched-chain keto acid
disease (MSUD) amino acids dehydrogenase
 VIL (Val, Iso, Leu)  Blocks brain transporter =
Mental retardation

Amino acid BREAKDOWN/CATABOLISM/ Transamination

 UREA Cycle
 Location: MITOCHONDRIAL MATRIX & CYTOSOL

End product of PROTEIN METABOLISM → Urea (Blood, Urea, Nitrogen)

Enzymatic defect in Urea cycle can result in intoxication most severe state
NITROGEN Metabolism:
o Ureotelic = Humans & Mammals
o Uricotelic = Reptiles & amphibians
 INSULIN GLUCAGON
 FED-state/ Produced during/after  FASTING-state/ produced during
meals starvation
 It Functions to reduce ↓  It Functions to increase ↑
glucose/sugar in the blood glucose/sugar in the blood
 Facilitates metabolic processes w/c  Facilitates metabolic processes w/c
breakdown of glucose produces/formation glucose
 ANABOLIC hormone/ Building up  CATABOLIC hormone/ Breaking down

Infos: INSULIN GLUCAGON

 Source Beta-cells islets of Langerhans Alpha islets of Langerhans
(PANCREAS) (PANCREAS)
 Structure 2 polypeptide chains w/ 51 AA Single/ 1 polypeptide chain w/ 29
linked together by 2 disulfide Amino acids.
bridge
 Stimulus for Ingestion/ ↑ of glucose & amino Actual/ Potential hypoglycemia
secretion acids(during Fed state or (fasting/ Starvation) takes effect
immediately after a meal) takes after more than 4 hours after a
effect during 4 hours after meal meal
 Pathways  Glucose uptake  Amino acid uptake
Increased/  GlycoLYSIS  GlucoNEOGENESIS
Stimulated  GlycoGENESIS  GlycogenoLYSIS
 Lipogenesis/ Fatty acid  Beta-OXIDATION/ LipoLYSIS
synthesis  KetoGENESIS
 Protein synthesis
 Pathways  Those who are listed by  Those who are listed by
decreased GLUCAGON INSULIN
 Similar effect to  N/A  Epinephrine, Cortisol, Growth Hormone

Concern INSULIN GLUCAGON (opposite)

Blood sugar ↓ Reduced/ Decreased ↑ Increased
Timing Fed state (kumain) Fasted state (dipa kumain)
Cell glucose uptake ↑ Inc N/A
Glycolysis ↑ Inc ↓ Dec
Fatty Acid Synthesis/ ↑ Inc ↓ Dec
Lipogenesis
Glycogenesis ↑ Inc ↓ Dec
Glycogenolysis ↓ Dec ↑ Inc
Gluconeogenesis ↓ Dec ↑ Inc
Ketogenesis ↓ Dec ↑ Inc
Lipolysis/ Betaoxidation ↓ Dec ↑ Inc
 METABOLIC INTEGRATION SUMMARY
Metabolic Pathway LOCATION/ Cellular Rate-limiting enzyme
site
Glycolysis Cytosol Phosphofructokinase
Glycogenesis Cytosol Glycogen synthase
Glycogenolysis/ Glycogen breakdown Cytosol Glycogen phosphorylase
Purine synthesis Cytosol Glutamine-PRPP amidotransferase
Pyrimidine synthesis Cytosol CPS-II /Carbamoyl phosphate
synthetase II
Pentose Phosphate Cytosol G6PD/ Glucose-6-phoshate
Pathway dehydrogenase
Fatty acid synthesis/ Cytosol & Smooth ER & Acetyl-CoA carboxylase
Lipogenesis Mitochondria
Cholesterol synthesis Cytosol (step 1) HMG-CoA Reductase
Smooth ER
Ketogenesis Mitochondrial matrix HMG-CoA Synthase
Beta-oxidation/ Mitochondrial matrix CAT-I/ Carnitin acyltransferase I
Lipolysis
ETC/ Electron Transport Chain Mitochondrial matrix
Kreb’s cycle/ TCA Mitochondrial matrix Isocitrate dehydrogenase
cycle/ Citric acid cycle
Gluconeogenesis Mitochondrial matrix(1-2) Fructose-1,6-biphosphate
Cytosol (Step 3-11)
Urea cycle Mitochondrial matrix(1) CPS-I/ Carbamoyl phosphate
Cytosol (Step 2-4) synthetase I

TABLE SUMMARY
Glycolysis Glycogenesis Cholesterol
synthesis
What it is for? ●Breakdown of glucose ●Synthesis of Glycogen
Where does it ●Cytosol ●Liver & Muscle ●Cytosol
occur/ location ●Cytosol ●All tissues
Substrate Glucose a-D-glucose Acetyl-CoA
End-products 2 molecules of Pyruvate Glycogen Cholesterol
Rate- limiting Occurs earlier than the rest Elongation of glycogen HMG CoA →
step(slowest) Step 3 (Fructose-6-PO₄) → chain (a-1,4) Mevalonate
Fructose 1,6-biPO₄
Rate limiting Phosphofructokinase Glycogen synthase HMG CoA →
enzyme Reductase
Energy yield 2 ATPs & 2 NADH
Irreversible step Step 1,3,10
 TABLE SUMMARY
Gluconeogenesis Glycogenolysis Ketogenesis
What it is for? ●Synthesis of glucose ●BREAKDOWN of ●Synthesis of
from non-carbohydrates glycogen to glucose Ketone bodies
● Prevents Hypoglycemia ●↑ glucose can cause ●Alternative fuel for
during fasting Diabetes mellitus peripheral tissues
Where does it ●Liver 90% & Kidney10% ●Liver & Muscle ●Liver
occur/ location ●Mitochondria & Cytosol ●Cytosol ●Mitochondria
Substrate ●Pyruvate (can Glycogen Acetyl CoA
metabolize into alcohol)
●Lactate
●Glycerol
●Certain amino acids
End-products Glucose ●Glucose in liver Ketone Bodies:
●Glucose-6-phosphate ●Acetone (can’t be
in muscle utilized for energy)
●Acetoacetate
●B-hydroxybutyrate
Rate- limiting Fructose 1,6-biphosphate Shortening of glycogen Acetoacetyl-CoA
step (slowest) (PO₄) chains → HMG CoA
Rate limiting Fructose 1,6- Glycogen HMG-CoA
enzyme bisphosphatase phosphorylase synthetase

TABLE SUMMARY
Kreb’s Cycle/ Citric Acid Pentose Phosphate Pathway/ PPP
What it is for? ●Central hub/ Major pathway ●Produces NADPH
formation of energy ●Produce Ribose-5-Phosp.
●ATP generation ●Provides mechanism for metabolic
of 5-carbon sugar
●Doesn’t produce nor consume ATP
Where does it Mitochondria/ Mitochondrial ● Cytosol
occur/ location matrix ● RBCs & tissues that lipids (liver,
adipose tissue, testes, thyroid,
adrenals)
Substrate Acetyl-CoA Glucose-6-phosphate
End-products 2 CO2, 1GTP, 1NADH 1FADH₂ ●NADPH ●Ribose-5-phosphate
Rate- limiting Step 3, Isocitrate Glucose-6-phosphate
step → 6-phosphogluconate
Rate limiting Isocitrate dehydrogenase G6PD/ Glucose-6-phosphogluconate
enzyme
Energy yield 10 ATP/ Acetyl
 TABLE SUMMARY
Lipolysis/ Beta-oxidation Lipogenesis Urea Cycle
What it is for? ●Breakdown of Fatty acids ●Synthesis of fatty acids ●Conversion of
●Produces acetyl CoA, (Palmitate FA) nitrogenous
FADH2 & NADH waste→ Urea
●can further fed into TCA
cycle
Where does it ●Beta-oxidation ●Fatty-acid Activation LIVER ONLY
occur/ location = Mitochondrial matrix = Cytosol Mito & Cytosol
Substrate Palmitate/ Even numbers Acetyl CoA NH3, Aspartate
saturated FA CO2
End-products Every cycle: 1 acetyl CoA, Palmitoyl-CoA Urea
FADH2 & NADH
Rate- limiting Translocation of Fatty acyl Acetyl CoA + HCO3
step CoA from cytosol to +ATP → Malanoyl CoA
Mitochondria
Rate limiting Carnitine-Palmitoyl Acetyl CoA Carboxylase
enzyme Transferase
Energy yield 2 ATPs spent from FA
1 ATPs produces from
beta-Oxidation

Glutelin = insoluble in water, neutral solvents, salts & alcohol but soluble in dilute
acid/base
Adenylyl creates cAMP from ATP while PDE degradtes it to ATM
Dinitrophenol (DNP) = Production of ATP is expected to be most impaired with
addition of this compound in mitochondrial sample

Name: Abnormal Chromosome

Patau Syndrome Trisomy 13
Edward-Warkany’s Trisomy 18
syndrome Trisomy 18
Down Syndrome Trisomy 21
Normal 22 Chromosomes