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
