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 pairsCats = 45 pairsTomato = 12 pairs

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

1.) Transport and Storage Examples:

Myoglobin (muscle) / Hemoglobin (blood) = Oxygen carriers Transferrin = Transport form of Iron (Fe) in the body Ferritin = Storage of Iron (Fe)

2.) Muscular Contraction Examples:

Actin and Myosin = Skeletal and Muscular contraction. Ca++ Dependent. 3.) Biological Catalyst

Enzymes 4.) Metabolic Control

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

IgA, IgD, IgE, IgG, IgF 6.) Tissue Differentiation

Stem Cells - Undifferentiated cells, Best Sources: Fertilized Egg, Placenta II. 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 MNEMONICS: Avon Lipstick

Alanine (-CH3)------------------ Ala, A Valine (Isopropyl)-------------- Val, V Leucine (Isobutyl)-------------- Leu, L Isoleucine (Sec-butyl)--------- Ile, I Proline (Cyclic)------------------ Pro, P

R= Thioether (R-S-R)

Methionine ------- Met, M

Polar Amino Acid:

A. R= Alcohol (-OH)

Serine --------- Ser, S Threonine ---- Thr, T

B. R= Amide

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 (4 Carbon Atoms) Glutamate ---------- Glu, E (5Carbon Atoms) *Polar

Basic Amino Acid:

Arginine ( Guanido = Sakaguchi's Test ) ---- Arg, R 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 InteractionsB.) Polar A.A. = ( Ser, Thr, Asn, Gln ) = H-BondsC.) 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 Proteins2.)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