Biochemistry = Biomolecule / Macromolecules

= Proteins, Nucleic Acid, Carbohydrates, Lipids

Cell - Basic unit of life
CELL
1.) Prokaryotic

No True Nucleus
Do not possess membrane bound organelles

Ex. Monera = Circular DNA, Plasmids , Ribosomes

2.) Eukaryotic

True nucleus
Membrane bound nucleus
Membrane bound organelles
Linear in the form of chromosomes

Ex. Protista, Fungi, Plantae, Animalia - Multicellular Eukaryotes

Matured RBC - No nuclei , Flexible without the nucleus

Erythrocytes - Possess nuclei, Baby RBC

Parts of Plant / Animal Cell

1.) Cell Membrane - Barrier; Protection

Fluid Mosaic model

Lipid Bi-layer

2 Types of Protein found on Cell Membrane:

1.) Peripheral - Protruding out of C.M. (Receptors)

2.) Integral - Embedded within the C.M. (Ion-Channels)

Semi-Permeable / Semi-Selective

Non-Polar Molecules = Passive Diffusion (NO ENERGY NEEDED)

Ex. H2O, O2,CO2

= Conc. Gradient

Polar Molecules = Facilitated Diffusion (NO ENERGY NEEDED)

Ex. Glucose

= Need the presence of Carrier Molecule / Protein

Ions = Active Transport (REQUIRES ENERGY)

Ex. Ion-Channels

= Against Conc. Gradient

CELL WALL (plants) = Cellulose - Rigidity

2.) Cytoplasm / Cytosol - Liquid portion of cell.

Organelles - "Organ like" structures

3.) Nucleus - "Control Center" of the cell.

"Brain"
DNA & RNA

4.) Mitochondria - "Powerhouse" of the cell

Location of ATP synthesis, Metabolic Pathway ( ETC, Kreb's Cycle, B Oxidation )

5.) Endoplasmic Reticulum :

a.) Smooth E.R. = Absence of Ribosomes

Sites of lipid / fatty acid synthesis

B.) Rough E.R. = Presence of Ribosomes

Sites of Protein Synthesis

6.) Golgi Bodies - Act as a storage sites.

Protein product undergoes Modification.

Ex. Glucosylation - Attachment of Carbohydrates to proteins.

7.) Ribosomes - Site of Protein Synthesis

Made of ribosomal RNA + other protein

Prokaryotes = 30s + 50s = 70s

*S = Svedberg (Unit of Sedimantation )

Eukaryotes = 40s + 60s = 80s

8.) Lysosomes - "Suicide Sacs"

Produces hydrolytic enzymes ( macrophages / phagocytes )

Peroxisomes - Specialist lysosomes that produce hydrogen peroxide.

9.) Chloroplast - Contain green pigment (Chlorophyll )

Mitosis

Cell Multiplication
Cytoplasmic Division
Somatic / Body cells
Diploid daughter cells (Complete #'s or sets of chromosomes)
Ex. Human: 46 chromosomes (23 pairs)
Division:
- 22 pairs Somatic
- 1 pair Sex Chromosomes : Female = XX , Male = XY

Meiosis

Cell division
Cytoplasmic & Nuclear sex cells / gametes
Haploid daughter cells (Half of the total #s of chromosomes)

Aneuploidy - Abnormality in the #'s of chromosomes

Trisomy 21 (Down's Syndrome)

21st pair is triplet
47 chromosomes
Excess chromosomes
Somatic chromosomes

XXX = Super female

47 chromosomes
Extra "X" Chromosomes
Sterile
Mentally retarded

Short life span

XXY = Klinefetter's Syndrome

Biological male but have certain female traits
Gynecomastia - Male with female breast
Male trait is suppressed
Hypogonadism - Small Testicles

Dogs = 36 pairs
Cats = 45 pairs
Tomato = 12 pairs

Proteins - polymers of amino acid that are joined by peptide bonds.

I.

Dynamic Functions
1.) Transport and Storage
Examples:

I.
II.
III.

Myoglobin (muscle) / Hemoglobin (blood) = Oxygen carriers

Transferrin = Transport form of Iron (Fe) in the body
Ferritin = Storage of Iron (Fe)
2.) Muscular Contraction
Examples:

IV.

Actin and Myosin = Skeletal and Muscular contraction. Ca++

Dependent.
3.) Biological Catalyst

V.

Enzymes
4.) Metabolic Control

VI.
VII.
VIII.
IX.
X.

Polypeptide hormone: Insulin & Glucagon = Central

carbohydrate metabolism
Oxytocin (Love Hormone) & Vasopressin (Anti Diuretics)
Somatotropins - Growth Hormones
Thyroid Hormones - T3, T4
FSH
5.) Immune System
Examples: Immunoglobulins

XI.

IgA, IgD, IgE, IgG, IgF

6.) Tissue Differentiation

XII.

Stem Cells - Undifferentiated cells, Best Sources: Fertilized Egg,

Placenta

I.

Structural Functions

Collagen - Skeletal Muscle

Elastin - Skeletal Muscle
Keratin - Hair, Nail
Fibrin - Silk, Spider web
Classification of Protein:
1.) Simple Protein - Amino Acid Only
Examples: Collagen, Elastin, Keratin, Fibrin

Albumin (Oval Bumin)

Glutelin (Glutein) - Plant Protein
2.) Conjugated Protein - Amino Acid + Organic / Inorganic components
Examples:

Nucleoproteins - with nucleic acids

Lipoproteins - with lipids
Glycoproteins - with carbohydrates (more protein)
Mucoproteins - with carbohydrates (more carbohydrates)
Chromoproteins - with metals; Not colored
Examples: Metallothioneins - Ca, Hg, Zn (Metallic poisoning)

Phosphoproteins - with phosphates other than Nucleic Acid

Examples: Casein - Milk
Classification of Amino Acids:
1.) Standard (Common) Amino Acid

One specific codon existing at DNA genetic code

Codon - sequence of 3 nucleotides specifying an amino acid
Examples: AUG (Start Codon) - Methionine

20 Standard Amino Acids

2.) Derived Amino Acids
Examples:

Hydroxyproline - component of Collagen

Hydroxylysine - cross link of collagen
Gamma Carboxyglutamate - 14 clotting factors
II (Prothrombin) --------> Thrombin
Glu
Gamma Carboxyglutamate
Cysteine: 2 Cystein
- SH + SH
- "S---S" ("Disulfide Bridge")
Alpha Amino Acids:

Non Polar Amino Acid:

R= Aliphatic

Alanine (-CH3)-----------------Valine (Isopropyl)-------------Leucine (Isobutyl)-------------Isoleucine (Sec-butyl)--------Proline (Cyclic)------------------

R= Thioether (R-S-R)

Methionine ------- Met, M

Polar Amino Acid:

A.

R= Alcohol (-OH)

A.
B.

Serine --------- Ser, S

Threonine ---- Thr, T

A.

R= Amide

MNEMONICS: Avon Lipstick

Ala, A
Val, V
Leu, L
Ile, I
Pro, P

Asparagine ----- Asn, N

Glutamine ------ Gln, Q

R= Thiol (-SH)

Cysteine ------ Cys, C

R= H

Glycine ------ Gly, G

Acidic Amino Acid:

Di Carboxylic acid / Salt Forms

Aspartate ----------- Asp, D

Glutamate ---------- Glu, E

Basic Amino Acid:

Arginine ( Guanido = Sakaguchi's Test ) ---- Arg, R

(4 Carbon Atoms)
(5Carbon Atoms) *Polar

Histidine (Imidazole) --------His, H

Lysine (Additional NH2) --- Lys, K

Aromatic Amino Acid:

Phenylalanine (Benzine) ------- Phe, F

Tyrosine (Phenol) --------------- Tyr, Y
Tryptophan (Indole) ------------ Trp, N
22 Amino Acids & Their Structures

Properties of Amino Acid:

1.) Amphoteric

Acts as Acid + Base

COOH - Acidic
NH2 - Basic

2.) Chirality / Optical Activity

Chiral "C" Centers

"C-C" Atoms w/ 4 different groups
Except: Glycine (R=H)

3.) Zwitterions / Dipolar Ions

Electrically Neutral
PI = Isoelectric point / PH
= PH at which Amino Acid exists in its Zwitterionic form
= PH at which the Amino Acid is electrically neutral.

UV Absorption

Aromatic Amino Acids : Phe, Tyr , His

Levels of Protein Organization / Structure

1.) Primary Level / Structure

Amino Acid sequence

NSQVKLWY
Biuret Test : Polypeptide determination

2.) Secondary Level / Structure

Formation of Hydrogen Bond in the peptide bond

Alpha Helix - 3.6 - 4 A.A. Residues ( Keratin ; Myoglobin /

Hemoglobin : 70% of Alpha Helix )
Beta Pleated Sheet - Fully extended polypeptide ( Fibrin : Strong
protein - Ala, Gly = Very Small )
Collagen Helix
Beta Tums / Loop
Random Coil

Alpha Helix

Collagen Helix :

Triple Helix
Contains 3 Alpha Helixes coiled together

Beta Turns / Loop

Type 1 B-Turn = Proline (Highly Flexible)

Type 2 B-Turn = Glycine (Highly Flexible)
Turn - Need at least : 4 Amino Acid Residue

Random Coil

No pattern

3.) Tertiary Level

3D structure
Interactions of R groups of Amino Acid
Examples:
A.) Non Polar A.A. = Hydrophobic Interactions
B.) Polar A.A. = ( Ser, Thr, Asn, Gln ) = H-Bonds
C.) Acidic A.A. = Negative ( - ) Ionic interaction
D.) Basic A.A. = Positive ( + ) Ionic Interactions

Very Strong Bond

Example: Insulin

Has 3 disulfide bond ( -S-S- )

If destroyed, It becomes inactive

Example: Keratin

Straight Hair = Lesser Cysteine

Rebonded Hair = Disulfide Reduction

4.) Quaternary Level / Structure

2 or more subunits or domain

Subunit / Domain - Polypeptide that folds independently

MYOGLOBIN

Single polypeptide
Tertiary level
Binds to 1 Oxygen ( O2 )
Heme = Porphyrin ring + Fe -----> O2

HEMOGLOBIN

Higher Molecular weight

Binds to 4 Oxygen ( O2 )
2 Subunits / Domains
Alpha Domain =
2 polypeptides
Beta Domain = + 2 polypeptides
4 polypeptides

SICKLE CELL ANEMIA

Genetic Disorder
Point Mutation ----> Hemoglobin Gene

Denaturation (Destruction) of : Quaternary , Tertiary and

Secondary with loss of function
Destruction of Primary: HYDROLYSIS

Examples of Denaturation:
1.) High Temperature

Irreversible

Ex: Hard Boiled Egg (white portion)

2.)Extreme PH

Interferes with ionic interactions

3.)Organic Solvents

Ex: Alcohols (-OH) interferes with Hydrogen Bonding

Hand Sanitizer
"-S-S-" ----> B-Mercaptoethanol

4.) Solutes

Urea (Interferes with Hydrogen bonding interaction)

Guanidine HCl (Interferes with Hydrogen bonding interaction)

Native Conformation

Normal, folded protein (functional)

Misfolding of proteins = Diseases

Protein Misfolding Diseases:

1.) Alzheimer's Disease

Amyloid Precursor Protein (APP)

2.) Bovine Spongiform Encephalopathy (BSE)

Mad Cow Disease - Restlessness and Stupor

Not sexually transmitted

Prions in humans - 90% identical to Prions of cows
Wagyu - Japanese Beef
Abnormal prion - Heat and protease resistant

3.) Creutzfeldt - Jakob's Disease

Spongiform encephalopathy
Misfolding

Chaperones - Protein that helps in the folding of other protein

1.) Heat-shock Proteins
2.)Chaperonins

Defect in chaperones causes misfolding

Purification of CHON
1.) Salting out

Protein will precipitate

Ex: (NH4)2SO4

2.) Dialysis

Dialysis membrane (molecular cut-off)

Molecular size
Ex: 6000 Da

3.) Chromatography
A.) Size Exclusion Chromatography

Gel filtration chromatography

Molecular size
SP: Polymer with different pore sizes heads

B.) Reversed Phase Chromatography

SP: Non Polar

MP: Polar
Hydrophobicityl Polarity
From most polar to most non polar ( Most polar ------> Non
polar )

C.) Ion Exchange Chromatography

Based charges
SP: Cation - Exchanger ( - )
Anion - Exchanger ( + )

D.) Affinity Chromatography

Antibodies
SP: Antigen (Ligand)

Gel Electrophoresis = Charge & Size

Cathode: ( - )
Anode: ( + )
SDS - PAGE
Sodium Dodecyl Sulfate (SDS) --> Anionic Surfactant
Polyacrylamide Gel Electrophoresis (PAGE)
From smallest to largest

Isoelectric Focusing

PI

Molecular Weight:

Matrix Assisted Laser Desorption Ionization (MALDI) - Time of

Flight (TOF)
Mass Spectroscopy