Biochemistry

TYPES OF TRANSPORT SYSTEMS

1. PASSIVE DIFFUSION
– No energy
– Higher to lower conc. (solute)
Driving force: Conc. Gradient

2. ACTIVE TRANSPORT
– Requires energy
– Lower to Higher conc. (solute)
Driving force: ATP

3. FACILITATIVE DIFFUSION
– No energy
– Utilizes a carrier (Usually a CHON)
Driving force: Conc. gradient
 TYPES OF TRANSPORT SYSTEMS
4. ENDOCYTOSIS
– Molecules go in the cell
A. PHAGOCYTOSIS
• Cell eating
• Involes the ingestion of LARGE particles such as viruses, bacteria,
cells, or debris
B. PINOCYTOSIS
• Cell drinking
• Property of all cells; It leads to the cellular uptake of fluid and
fluid contents

5. EXOCYTOSIS
– Involves the release of macromolecules to the exterior.
 CELL
PROKARYOTES EUKARUYOTES

DO NOT HAVE TRUE NUCLEUS HAVE TRUE NUCLEUS

NO MEMBRANE BOUND ORGANELLES HAVE MEMBRANE BOUND ORGANELLES

ONLY RIBOSOMES ARE PRESENT HAVE A LOT OF VARIOUS ORGANELLES

PRESENT
 PARTS OF THE CELL
1. CELL MEMBRANE
– Acts as a barrier/For protection
– Semi-permeable/Semi-selective
➢ Fluid Mosaic model: “Cell membranes are composed
of a lipid bilayer”

2. CYTOPLASM/CYTOSOL
– Liquid portion of the cell
– Organelles are present here

3. NUCLEUS
– Control center/Brain of the cell
– Where genetic material is contained
 PARTS OF THE CELL
4. MITOCHONDRIA
– Powerhouse of the cell
– Where ATP synthesis occurs
– Organ for respiration
Processes that occur here:
a. Kreb’s cycle
b. ETC
c. –oxidation of fatty acids

5. ENDOPLASMIC RETICULUM
A. SMOOTH ER
• No ribosomes attached
• Site of fatty acid synthesis
B. ROUGH ER
• Ribosomes are attached to the surface
• Site of CHON synthesis
 PARTS OF THE CELL
6. GOLGI APPARTUS
– Storage sites of CHON
– Responsible for POST TRANSLAIONAL MODIFICATION

7. RIBOSOMES
– Composed of ribosomal RNA + CHONS
A. Bacterial subunits
• 30s
• 50s
B. Eukaryotic subunits
• 40s
• 60s
 PARTS OF THE CELL
8. LYSOSOMES
– Suicide sacs of the cell

➢ PEROXISOMES- Specialized lysosomes that

produce H2O2

9. CHLOROPLASTS
– Only present in plants
– Chlorophyll
 CELL CYCLES
MITOSIS MEIOSIS

CELL MULTIPLICATION CELL DIVISION

CYTOPLASMIC DIVISION CYTOPLASMIC AND NUCLEAR DIVISION

OCCUR

SOMATIC/BODY CELLS SEX CELLS/GAMETES

DAUGHTER CELLS ARE DIPLOIDS DAUGHTER CELLS ARE HAPLOIDS

PROTEINS
 PROTEINS
• Came from the Greek word “PROTEIOS” meaning “pre-
eminence” or “of first importance”
• Polymers of amino acids joined by PEPTIDE BONDS
• LITMUS PAPER: Red-Blue

I. DYNAMIC FUNCTIONS
A. TRANSPORT STORAGE
– Ex: Myoglobin & Hemoglobin
Transferrin
Ferritin
B. MUSCULAR CONTRACTION
– Ex: Actin & Myosin
C. BIOLOGICAL CATALYSTS
– Ex: Enzymes
 PROTEINS
D. METABOLIC-CONTROL
– Ex: Hormones
E. IMMUNE SYSTEM
– Ex: Immunoglobulins
F. TISSUE DIFFERENTIATION
– Ex: Tumor necrosis factor
Interleukins

II. STRUCTURAL FUNCTIONS

Ex:
Collagen & Elastin-
Keratin-
Fibroin-
 CLASSIFICATION OF PROTEINS
I. ACCORDING TO HYDROLYSIS PRODUCTS

1. SIMPLE PROTEINS
– These are true proteins
– On hydrolysis, they yield -amino acids and their
derivatives
 GROUP SOLUBILITY EXAMPLES
ALBUMINS SOL. IN: WATER & DILUTE NEUTRAL SALT Serum albumin- Blood
SOLUTIONS Lactalbumin- Milk
Ovalbumin- Egg white
GLOBULINS SOL. IN: NEUTRAL DILUTE SALT SOLUTIONS Ovoglobulin- egg white
INSOL.IN: WATER Edestin- hempseed
Legumin- peas
Myosinogen- muscles
Serum globulin- Blood

GLUTELINS SOL.IN: DILUTE ACIDS AND ALKALIES Glutenin- Wheat

INSOL. IN: NEUTRAL SOLVENTS Oryzenin- Rice
PROLAMINES SOLUBLE IN: 70% ALCOHOL Gliadin- Wheat
INSOLUBLE IN: ORDINARY SOLVENT Zein- Corn
Hordein- barley
HISTONES SOL.: WATER, DILUTE ACIDS & ALKALIES Globin- Hemoglobin
INSOL. IN: DILUTE AMMONIA Thymus histone
Srobrone- Mackerel
PROTAMINES SOL. IN: WATER, DILUTE ACIDS &ALKALIES Salmin- Salmon sperms

SCLEROPROTEINS SOL. IN: WATER AND NEUTRAL SOLVENTS Keratin- epidermal tissues
Elastin- ligaments
Collagen- Hides, bons, and
cartilages
 CLASSIFICATION OF PROTEINS
2. CONJUGATED PROTEINS
– Made up of protein molecules combined with
non-protein groups
GROUPS COMPOSED OF: EXAMPLES
NUCLEOPROTEINS CHON+NUCLEIC ACIDS Chromatins
GLYCOPROTEINS CHON+CHO Mucin- saliva
Tendomucoid- tendons
Osseomucoid- bones
PHOSPHOPROTEINS CHON+PHOSPHATE Casein- milk
Vitelin- egg yolk
CHROMOPROTEINS CHON+COLORED METALS Hemoglobin
Cytochromes
Rhodopsin
LIPOPROTEINS CHON+FATS
 CLASSIFICATION OF PROTEINS
3. DERIVED PROTEINS
– Include substances formed from simple and
conjugated proteins
 DIVISION GROUPS DESCRIPTION EXAMPLES
1. PRIMARY PROTEIN A. PROTEANS Insoluble substances Myosann- myosin
DERIVATIVES resulting from the Edestan- edestin
preliminary action of
water, dilute acids, or
enzymes
B. METAPROTEANS Products of further Acid metaproteans-
hydorylsis acid albuminated
Alkali metaproteans-
alkali albuminate
C. COAGULATED Result from either: Cooked egg albumin
PROTEINS •Action of heat Cooked meat
•Alcohol
•UV rays
•Mechanical shaking
2. SECONDARY A. PRIMARY PROTEOSES
PROTEIN DERIVATIVES
B. SECONDARY
PROTEOSES
C. PEPTONES
D. PEPTIDES
CLASSIFICATION OF AMINO ACIDS
I. NONPOLAR AMINO ACIDS
A. ALIPHATIC CHAIN
1. Alanine - Methyl
2. Valine - Isopropyl
3. Leucin - Isobutyl
4. Isoleucine - Tert-butyl
B. THIOETHER
1. Methionine -Sulfur
 CLASSIFICATION OF AMINO ACIDS
II. POLAR AMINO ACIDS
A. ALCOHOL CONTAINING (-OH)
1. Serine
2. Threonine
B. THIOL GROUP
1. Cysteine -SH
C. AMIDE CONTAINING
1. Asparagine -___C
2. Glutamine -___C
D. HYDROGEN
1. Glycine -H
 CLASSIFICATION OF AMINO ACIDS
III. ACIDIC AMINO ACIDS (Additional COOH)
1. Aspartic acid/Aspartate -___C
2. Glutamic acid/Glutamate -___C

IV. BASIC AMINO ACIDS

1. Histidine -Imidazole ring
2. Arginine -Guanidino
3. Lysine - Epsilon amino group

V. AROMATIC AMINO ACIDS

1. Phenylalanine -Phenyl group
2. Tyrosine -Phenol group
3. Tryptophan -Indole ring
 TESTS FOR AMINO ACIDS
TEST REAGENTS USED EXPECTED (+) RESULT FOR
MILLON’S TEST Mercurous nitrate in OLD ROSE PPT TYROSINE
HNO3

BIURET TEST CuSO4 ROSE-PINK TO VIOLET PEPTIDE

LINKAGES

HOPKIN COLE’S REACTION Glycooxylic acid and VIOLET RING TRYPTOPHAN

conc. H2SO4

XANTHOPROTEIC REACTION HNO3 YELLOW-ORANGE PPT AROMATIC

AMINO ACIDS

TEST FOR SH GROUP Lead acetate BLACK PPT CYSTINE

CYSTEINE
METHIONINE
LIEBERMANN’S TEST Conc. HCl, sucrose VIOLET COLOR TRYPTOPHAN
sol’n
MOLISCH’S TEST H2SO4 VIOLET RING GLYCOPROTEIN

NINHYDRIN REACTION Triketohydrindene hydrate VIOLET COMPLEX -AMINO GROUP

(RUHEMANN’S
PURPLE)
SAKAGUCHI - naphthol and sodium RED-ORANGE ARGININE
REACTION hypochlorite COMPLEX
NITROPRUSSIDE TEST Sodium nitroprusside, RED COLOR CYSTEINE
dilute ammoniacal sol’n

FOLLIN’S REACTION 1,2 naphthoquinone-4- DEEP RED COLOR RAPID QUANTITATIVE

sulfonate, Sodium ESTIMATION OF
hydrosulfite AMINO ACIDS

SULLIVAN’S TEST 1,2 naphthoquinone-4- RED COLOR RAPID QUANTITATIVE

sulfonate, Sodium ESTIMATION OF
hydrosulfite AMINO ACIDS AFTER
REDUCTION

PAULY REACTION Diazotized sulfanilic acid RED COLOR HISTIDINE AND

TYROSINE
 PROPERTIES OF AMINO ACIDS
1. AMPHOTERIC
2. CHIRALITY/OPTICAL ACTIVITY
– Each C is attached to 4 different groups
Except: Glycine
3. ZWITTERIONS/DIPOLAR IONS
– Electrically neutral
4. UV ABSORPTION
– Aromatic amino acids only
 PROTEIN ORGANIZATION
1. PRIMARY LEVEL/STRUCTURE
– Amino acid sequence
– Formation of peptide bonds
2. SECONDARY LEVEL/STRUCTURE
– Repetitive structures
– Hydrogen bonding
A. -Helix
• Ex: Keratin & myoglobin
B. -sheet
• Highly compact=Strong
• Ex: Fibroin
C. Collagen helix
• Triple helix; very rigid
D. -turns
• Connects 2 secondary structures
2 groups:
1. Type I- Glycine
2. Type 2- Proline
 PROTEIN ORGANIZATION
3. TERTIARY LEVEL/STRUCTURE
– 3D structure
– Due to interactions of R groups of amino acids
4. QUATERNARY LEVEL/STRUCTURE
– 2 or more subunits/domains
 PROTEIN DENATURATION
DENATURATION:
– Destruction of the quaternary, tertiary, or
secondary structure with loss of function
• Agents causing denaturation:
1. High temp- results to irreversible denaturation
2. Extreme pH
3. Organic solvents
4. High salt concentration
ENZYMES
 ENZYMES
• Complex organic compounds that are biological
catalysts w/o being affected in the process.
• Most are protein in nature
➢ Co-enzyme
– Non protein group in an enzyme
➢ Apoenzyme
– Protein portion of an enzyme
➢ Holoenzyme
– Protein portion plus bound factor/prosthetic group
– Active form
➢ Zymogen (Pro-)(-gen)
– Inactive form of an enzyme
– Can be activated
 PROPERTIES OF ENZYMES
1. Catalytic activity
2. Specificity (1:1)

MODELS FOR ENZYME-SUBSTRATE

BINDING
1. LOCK & KEY MODEL
– Based on shape selectivity
Drawback: Assumes that enzyme is rigid
2. INDUCED FIT MODEL
– When enzyme is not yet active, it assumes a shape. Then
when bound, the shape changes.
3. TRANSITION STATE ANALOG MODEL
– There is a state existing between the reactants and the
products.
 ENZYME CLASSIFICATION
1. OXIDOREDUCTASES
– Redox transfer
Ex: Dehydrogenases
2. TRANSFERASES
– Catalyze group transfer reactions
Ex: Kinase, DNA polymerase
3. HYDROLASES
– Involved in hydrolytic cleavage reactions
Ex: Nucleases, Lipases, Amylases, Proteases
 ENZYME CLASSIFICATION
4. LYASES
– Involved in nonhydrolytic cleavage reactions
a. Breaking of a double bond by the introduction of a
funtional group
b. Formation of a double bond by the removal of a functional
group
Ex: Carbonic anhydrase
5. ISOMERASES
– Involved in rearrangement
reactions/interconversions of isomers
Ex: Mutases
6. LIGASES
– Involved in condensation reactions
Ex: Synthases, synthetases
NUCLEIC ACIDS
 NUCLEIC ACIDS
• Polymers of nucleotides joined together by
PHOSPHODIESTER BONDS.
2 CLASSES OF NUCLEIC ACIDS:
CLASS DNA RNA
SUGAR COMPONENT Deoxyribose Ribose

NITROGENOUS BASE Adenine & Guanine Adenine & Guanine

(PURINE)

NITROGENOUS BASE Cytosine & Thymine Cytosine & Uracil

(PYRIMIDINE)

CELLULAR LOCATION Nucleus & Nucleus & cytosol

mitochondria
NITROGENOUS BASES
 NUCLEIC ACID STRUCTURAL
ORGANIZATION
1. PRIMARY
• Gives the sequence of bases or nucleotides and
their relative contents or % composition in h DNA
molecule

2. SECONDARY
• Double helical structure resulting from H-
bonding interaction between bases
 BASE PAIRING RULE
• Purines can only pair with Pyrimidines via
hydrogen bonds
➢ Watson & Crick
– Suggested that the 3D structure of DNA is a double
helix

CHARGAFF’S RULE
– Adenine must pair with Thymine
– Guanine must pair with Cytosine
– Their amounts in a given DNA molecule will be about
the same
NUCLEIC ACID STRUCTURAL FEATURES
➢ RNA- Transmitters of the genetic information stored in the
DNA

1. mRNA
– Serves as the template for synthesis of proteins
– Carrier of codons or sequence of three bases specifying an
amino acid

2. rRNA
– Forms a complex with proteins to form the ribosomes which is
the site of protein biosynthesis

3. tRNA
– Contains the anti-codon and is the adaptor molecule for amino
acids
 CENTRAL DOGMA OF GENETICS
• E. coli was used

DNA RNA PROTEINS

DNA
 THE GENETIC CODE
• Genetic information is coded in form of base sequences
• A sequence of 3 bases in mRNA codes for a single amino
acid
• Codon is a triplet

Properties of the Genetic code:

a. Genetic code is degenerate

b. Genetic code is universal

c. It is non-overlapping

d. It is comma less
 THE GENETIC CODE
e. It is collinear

f. There are three stop codons to stop protein

synthesis. They do not code for any amino
acids and they act as releasing factors

g. AUG is the initiation codon

 MUTATION
• Changes in the nucleotide sequence of DNA
• May occur in somatic cells (Aren’t passed to
offspring)
• May occur in gametes (eggs and sperm) and
be passed to offspring
 TYPES OF MUTATIONS
1. CHROMOSOME MUTATIONS
– May involve:
a. Changing the structure of a chromosome
b. The loss or gain of part of a chromosome
i. Deletion
• Involved the loss of all or part of a chromosome
ii. Duplication
• Involves the production of extra copies of parts of the
chromosome
iii. Translocation
• When one part of a chromosome breaks off and attaches to
another chromosome
iv. Inversion
• Chromosome segment breaks off, flips around backwards. And
reattaches
v. Nondisjunction
• When homologous chromosomes fail to separate properly
during meiosis
 TYPES OF MUTATIONS
2. GENE MUTATION
– Change in the nucleotide sequence of a gene
– May be due to copying errors, chemicals, viruses,
etc.
a. Point mutation
• A single point in the DNA sequence is affected
• Can be a substitution in which one base is changed into
another base
i. Transition
– A purine substitutes a purine or a pyrimidine substitutes a
pyrimidine
ii. Transversion
– A purine substitutes a pyrimidine or a pyrimidine
substitutes a purine
 TYPES OF MUTATIONS
• Substitutions can lead to:
i. Missense mutation
– Change in a codon to one that encodes for a different amino
acid
ii. Silent mutation
– Change in a codon to one that encodes the same amino acid
iii. Nonsense mutation
– Change in an amino-acid-coding codon to a stop-codon

b. Frameshift mutations
• A single gene or nitrogen base is deleted or added from the
mRNA sequence causing a shift in the reading frame of the
genetic message
• Can be an insertion or deletion in which on base is inserted
or deleted in the DNA sequence
VITAMINS
 VITAMINS
FAT SOLUBLE VITAMINS
1. VITAMIN A
– RETINOIC ACID/RETINOL
– 1st vitamin discovered and the MOST TOXIC
Body functions:
• Synthesis of epithelial tissue
• Important for growth and reproductions as well as vision in
dim light
Deficiency:
• Nyctalopia or Night blindness
• Xerophthalmia
• Keratinization of tissues
• Sterility
Uses:
• Anti-oxidant for acne and wrinkles
 VITAMINS
2. VITAMIN D
– D2: ERGOCALCIFEROL
– D3: CHOLECALCIFEROL
– “Sunshine vitamin”
Body functions:
• Calcium homeostasis
Deficiency
• Rickettsia
• Osteomalacia
Uses:
• Anti-rachitic
 VITAMINS
3. VITAMIN E
– α-TOCOPHEROL
– “Anti-sterility vitamin”
– “Vitamin X”
Body functions:
• Anti-oxidant
• Increases skin elasticity
• Increased sexual vitality and vigor
Deficiency:
• Sterility
• Adverse effects in CNS, CV, reproductive, and
hematopoietic systems
 VITAMINS
4. VITAMIN K1
– K1: PHYTONADIONE
– K2: MENAQUINON
– K3: MENADIONE
– K4: MENADIOL
Body functions:
• Promote synthesis of clotting factors
Deficiency:
• Hemorrhage
 VITAMINS
WATER SOLUBLE VITAMINS
1. VITAMIN C
– ASCORBIC ACID/CEVITAMIC ACID
– Least stable vitamin
Body functions:
• Hydroxylation and amidation reactions
• Collagen synthesis
• Biotransformation; Absorption of iron
Deficiency
• Scurvy
• Loss of dental cement
• Hemorrhage
Uses:
• Anti-scorbutic
• Anti-oxidant
 VITAMINS
2. VITAMIN P
– HESPERIDIN & RUTIN; CITRIN
– Permeability factor
Body function:
• Capillary fragility permeability
Deficiency:
• Decreased capillary resistance
 VITAMINS
3. VITAMIN B1
– THIAMINE
– Thermolabile
Body function:
• Involved in protein synthesis
Deficiency:
• Beri-beri (polyneuritis)
• Wenicke-korsakoff syndrome
 VITAMINS
4. VITAMIN B2
– RIBOFLAVIN/LACTOFLAVIN/VITAMIN G
– Stains the urine
Body functions:
• Redox reactions
Deficiency:
• Cheilosis
• Stomatitis
• Glossitis
• Seborrheic dermatitis
 VITAMINS
5. VITAMIN B3
– NIACIN/NIACINAMIDE/NICOTINIC
ACID/NICOTINAMIDE
– P-p factor (Pellagra preventive factor)
– Most stable vitamin
Body functions:
• Redox reactions
Deficiency:
• Pellagra
• 3 D’s: Dermatitis, Diarrhea, Dementia
Use:
• Skin whitening
• Anti-hyperlipidemic
 VITAMINS
6. VITAMIN B4
– CHOLINE
– Nitrogenous base fund in lecithin
Body functions:
• Transport and utilization of fats
• Methylating agent in formation of creatinine
 VITAMINS
7. VITAMIN B5
– PANTHENOL/PANTOTHENIC ACID
– “Chick anti-dermatitis factor”
Body function:
• Structural component of Acetyl CoA
Deficiency:
• Fatigue
• Impaired coordination and irritability
• Burning foot syndrome
Use:
• Ingredient of shampoos
 VITAMINS
8. VITAMIN B6
– PYRIDOXINE/PYRIDOXAMINE/PYRIDOXAL PHOSPHATE
Body function:
• Protein metabolim
Deficiency:
• Convulsions
• Peripheral neuritis
• Microcytic anemia
Use:
• Antidote for Isoniazid poisoning
 VITAMINS
9. VITAMIN B7
– BIOTIN/VITAMIN H/COENZYME R
Body function:
• Fat and carbohydrate metabolism
Deficiency:
• Alopecia
• Anorexia
• Memory loss
• Mental depression
 VITAMINS
10. VITAMIN B8
– INOSITOL
– “Anti gray hair factor”
Body function:
• Synergistic and lipotropic effect of choline
 VITAMINS
11. VITAMIN B9
– FOLIC ACID/FOLACIN/PTEROYL GLUTAMATE
(PGA)/LEUCOVORIN
– “Anti-cancer derivative”
Body function:
• Purine & pyrimidine synthesis
Deficiency:
• Megaloblastic anemia
 VITAMINS
12. VITAMIN B12
– CYANOCOBALAMIN
Body function:
• Nucleic acid synthesis
• Myelin synthesis
Deficiency:
• Megaloblastic anemia
• Pernicious anemia
Use:
• Utilized in cancer radiation therapy
DIGESTION
 DIGESTION
• A process which is hydrolytic in nature and
catalyzed by enzymes in which complex food
material is changed into simple molecules which
can be absorbed, metabolized, and excreted
CARBOHYDRATES PROTEINS

1. MOUTH: 1. STOMACH
-by salivary amylases (ptyalin) -By pepsin when pepsinogen is
-Products: Oligosaccharides activated

2. STOMACH: 2. SMALL INTESTINE:

-By acid hydrolysis - By pancreatic proteases

3. SMALL INTESTINE
-by pancreatic amylases
 ABSORPTION
• The passage of end products of digestion from
the small intestine into the bloodstream
• Digested food normally remains in the small
intestines from 5 up to 8 hours.
 METABOLISM
• Sum total of chemical reactions needed to
maintain the functional and nutritional activities
in the living cell
2 ROUTES OF METABOLISM
1. Exogenous route
– Involves the use of food particles and their oxidation
to PRODUCE ENERGY
2. Endogenous route
– Involves food particles becoming PARTS OF BODY
TISSUES
 METABOLISM
2 PHASES OF METABOLISM
1. CATABOLISM
– Involves energy-releasing reactions/processes
– Includes all metabolic reactions with the
BREAKDOWN or DEGRADATION of biomolecules.
2. ANABOLISM
– Involves energy-requiring processes
– Requires enzymatic SYNTHESIS of relatively large
molecular components
 METABOLISM
4 STAGES OF CATABOLISM
I. Breakdown of biomolecules
– CHO Monosaccharides
– CHON Amino acids
– FATS Fatty acids+Glycerol
II. Further degradation of the molecule
III. TCA/Kreb’s cycle/Citric acid cycle
IV. ETC
METABOLISM OF CARBOHYDRATES
1. GLYCOLYSIS
– Breakdown of Glucose/Glycogen to Pyruvate
2. GLYCOGENESIS
– Synthesis of Glycogen from Glucose
3. GLYCOGENOLYSIS
– Breakdown of Glycogen to Glucose
4. GLUCONEOGENESIS
– Conversion of non CHO precursor to Glucose