1 BIOCHEM 1a LECTURE 1: PROTEINS (AMINO ACIDS) PROTEINS: AMINO ACIDS I. TWO TYPES OF PROTEINS II. FUNCTIONS OF PROTEINS III. AMINO ACIDS IV. EFFECT OF pH ON PROTEINS V. PEPTIDE BOND FORMATION VI. DEFINITION OF TERMS ORDER OF PROTEIN STRUCTURES I. PRIMARY STRUCTURE II. SECONDARY STRUCTURE III. TERTIARY STRUCTURES IV. QUARTERNARY STRUCTURES OTHER CONCEPTS IN PROTEINS I. DETERMINATION OF PRIMARY STRUCTURES OF PROTEINS II. PROTEIN FOLDING II. STUDYING THE TERTIARY STRUCTURES OF PROTEINS IV. DISEASES RELATED TO PROTEIN FOLDING V. EXAMPLES OF PROTEINS LECTURE 2: CARBOHYDRATES CARBOHYDRATES I. FUNCTIONS OF CARBOHYDRATES II. REQUIREMENTS TO BE CONSIDERED A CARBOHYDRATE II. DISEASES INVOLVED IN CHO METABOLISM SOME IMPORTANT CARBOHYDRATES I. MONOSACCHARIDES II. DISACCHARIDES III. POLYSACCHARIDES CHARACTERISTICS OF CHO I. STRUCTURES OF CARBOHYDRATES II. CARBOHYDRATE DERIVATIVES III. SUGARS HAVE REDUCING PROPERTIES IV. CARBOHYDRATES IN THE CELL MEMBRANE LECTURE 3: LIPIDS LIPIDS I. FUNCTIONS OF LIPIDS: II. FATTY ACIDS III. TRIACYLGLYCEROLS (TRIGLYCERIDES) LIPID CLASSIFICATION I. PHOSPHOLIPIDS II. GLYCOLIPIDS III. CHOLESTEROL LECTURE 4: BIOENERGETICS BIOENERGETICS I. LAWS OF THERMODYNAMICS II. METABOLISM III. FREE ENERGY (G) IV. STEPS IN HARNESSING ENERGY FROM FOOD V. SYNTHESIS OF ATP
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BIOCHEM 1a
LECTURE 1: PROTEINS (AMINO ACIDS)
PROTEINS: AMINO ACIDS
I. TWO TYPES OF PROTEINS II. FUNCTIONS OF PROTEINS
III. AMINO ACIDS
IV. EFFECT OF pH ON PROTEINS V. PEPTIDE BOND FORMATION
VI. DEFINITION OF TERMS
ORDER OF PROTEIN STRUCTURES
I. PRIMARY STRUCTURE
II. SECONDARY STRUCTURE III. TERTIARY STRUCTURES
IV. QUARTERNARY STRUCTURES
OTHER CONCEPTS IN PROTEINS I. DETERMINATION OF PRIMARY STRUCTURES OF PROTEINS
II. PROTEIN FOLDING II. STUDYING THE TERTIARY STRUCTURES OF PROTEINS
IV. DISEASES RELATED TO PROTEIN FOLDING
V. EXAMPLES OF PROTEINS
LECTURE 2: CARBOHYDRATES
CARBOHYDRATES
I. FUNCTIONS OF CARBOHYDRATES II. REQUIREMENTS TO BE CONSIDERED A CARBOHYDRATE
II. DISEASES INVOLVED IN CHO METABOLISM
SOME IMPORTANT CARBOHYDRATES I. MONOSACCHARIDES
II. DISACCHARIDES III. POLYSACCHARIDES
CHARACTERISTICS OF CHO
I. STRUCTURES OF CARBOHYDRATES II. CARBOHYDRATE DERIVATIVES
III. SUGARS HAVE REDUCING PROPERTIES
IV. CARBOHYDRATES IN THE CELL MEMBRANE
LECTURE 3: LIPIDS
LIPIDS
I. FUNCTIONS OF LIPIDS: II. FATTY ACIDS
III. TRIACYLGLYCEROLS (TRIGLYCERIDES)
LIPID CLASSIFICATION I. PHOSPHOLIPIDS
II. GLYCOLIPIDS III. CHOLESTEROL
LECTURE 4: BIOENERGETICS
BIOENERGETICS
I. LAWS OF THERMODYNAMICS II. METABOLISM
III. FREE ENERGY (G) IV. STEPS IN HARNESSING ENERGY FROM FOOD
V. SYNTHESIS OF ATP
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LECTURE 1: PROTEINS (AMINO ACIDS)
PROTEINS: AMINO ACIDS -most important in terms of function of cell
-polypeptide that has attained a unique stalk 3-D Shape (Conformation) which is functional (Native)
-amino acid sequence and shape determines function
-sequence is based on information coming from the gene
I. TWO TYPES OF PROTEINS
A. Simple Proteins
-contain only Amino Acids and no other Chemical Groups
-ex) Ribonuclease, Chymotrypsin
B. Complex Proteins
-has some other chemical component (Prosthetic Group)
-ex) Lipoproteins -Lipids -ex) Lipoprotein
Glycoproteins -Carbohydrates -ex) Globulin of Blood
Phosphoproteins -Phosphate -ex) Casein of Milk
Hemoproteins -Heme -ex) Hemoglobin
Metalloproteins -Iron, Zinc -ex) Ferritin,
II. FUNCTIONS OF PROTEINS
Catalytic Role: Enzymes
Antibodies of Immune System: Immunoglobulins, Interferon
Transporters to more materials around: Hemoglobin, Albumin, Lipoprotein
Regulators: Hormones, Insulin, Calmodulin
Structural Roles: Collagen, Elastin, Keratin
Agents of Motion: Cilia, Flagella, Muscles
Contraction: Actin, Myosin
Receptors: Glycophorin, LDL Receptor
Gene Regulation: Histones, Repressor Proteins
Nutrient and Storage Role: Casein (Milk)
III. AMINO ACIDS (Monomers of Proteins)
A. Structure Components of Amino Acids:
o Amino Group
o Carboxyl Group
o Chiral Carbon
o R-Group
B. Configuration Vs. Conformation
**Conformation -3-D arrangement / architecture of the protein
**Configuration -Geometric arrangement between a given set of atoms
-ex) D-Alanine, L- Alanine
L-Sterioisomer: predominant in nature, beneficial to life
D-Sterioisomer: toxic to life
Dextrotatory AA
Levorotatory AA: present in mammals as free AA and is not incorporated in proteins
-changing pH will alter the charge of a protein -this alters solubility and may change the shape of the protein (may cause denaturation)
Decrease pH : Net Charge = (+)
pH 7 : Net Charge = 0
Increase pH : Net Charge = (-) A. Titration of Amino Acids pK1 -Ionization of Proton attached to Carboxyl Group
PK2 -Ionization of Proton attached to NH3+
pK3 -Ionization of Proton attached to R-groups
**Polar Environment -favors R-COO- and R-NH3+
**Non-Polar Environ. -favors RCOOH and RNH2
B. Zwitterion Molecule -Net Charge of Region = 0
-not migrate toward either cathode or anode **pI = Isoelectric Point -point where Amino Acid has a Net Charge = 0 (important for diagnosis)
C. Amino Acids as a Buffer -Buffer Region is equal to +1, -1 of a pK value (at the point where there is 50:50 Ratio)
-at pK values, 50% of Amino Acid Ionized, and 50% has not, therefore, 50% is a Proton Donor, and 50% is a Proton Acceptor; this region is a good Buffer
**Amphoteric -capable of donating a Proton (Acid) and accepting a Proton (Base) **Buffer -resists drastic change in pH
V. PEPTIDE BOND FORMATION -Carboxyl Group of Previous A.A. forms a covalent bond with Amino Group of next A.A
-formed during protein synthesis
-interactions will now be done by the R-Groups because Nt and Ct are involved in Peptide Bonds
-amino acids in polypeptides are called Aminoacyl Residues
-peptide bonds are uncharged at any pH
A. Characteristics of Peptide Bonds (Trans-Peptide Bonds)
Peptide Bonds have partial Double Bond Characters (Cannot rotate)
Psi Bonds (between Alpha-Carbon and Carboxyl Atom) can rotate
Phi Bonds (between Amino Group and Alpha-Carbon) can rotate
B-Hairpin Motif: 2 beta sheets which are anti parallel
A-A Motif
B- Barrels
IV. QUARTERNARY STRUCTURES
-requires more than one polypeptide
-stabilized by non-covalent interactions: Hydrophobic Interactions, Electrostatic / Ionic Bonding, Van der
Waal’s, Hydrogen Bonding)
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OTHER CONCEPTS IN PROTEINS
I. DETERMINATION OF PRIMARY STRUCTURES OF PROTEINS
-before a protein is studied, it should be in its simplest form -we must first determine a protein’s primary structure
A. Electrophoesis -separated according to charge (anode vs. cathode)
-clear bonds signify successful purification -separation of charged molecules based on rates of migration
B. Gel Filtration -small molecules come out last
-separation based on Stoked Radius (diameter of sphere as they tumble in solution)
C. Other Methods
Column Chromatography
Partition Chromatography
Absorption Chromatography
Ion Exchange Chromatography
Hydrophobic Interaction Chromatography
Affinity Chromatography
II. PROTEIN FOLDING -polypeptides are helped by Chaperones for correct folding of protein -when proteins are being synthesized, they are already being helped
-folding of proteins is spontaneous, but sometimes, wrong folding occurs -system in cells where other proteins help proteins fold (chaperone)
-Aggregates are proteins which have failed to refold spontaneously **Chaperones -necessary for proper tridimentional structure of protein
-maintains the proteins in unfolded state while protein synthesis takes place -inhibits unnecessary protein-protein interactions
Enclosed Forming Protein Chaperones Help in Folding Protein is Released
**Denaturation of Proteins -unfolding of proteins **Aggregates -proteins which have failed to refold spontaneously
III. STUDYING THE TERTIARY STRUCTURES OF PROTEINS -to study the tertiary structure, we must get protein at its native structure
A. X-Ray Crystallography
-used to measure DNA structure -proteins are crystallized then X-rayed -precipitation of a protein under condition in which it forms crystals that defract X-rays
-with a film, tertiary structure can be studied (no computers!) B. Nuclear Magnetic Resonance Spectroscopy
-measures the absorbance of radio frequency electromagnetic energy
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C. Molecular Modeling
IV. DISEASES RELATED TO PROTEIN FOLDING
A. Alzheimer’s Disease
-B-Amyloid Proteins change into plaques
-40 residue segment cleaved from precursor protein
-change from Alpha Helix to Beta Sheet (because of 4 genes)
-destroys the Hypoccampus
B. Madcow’s Disease
-Alpha Helices are transformed into Beta Sheets
-Prions are infected (infectious protein w/o nucleic acid)
PrP (Prion Relative Proteins) -Alpha Helix
PrPSc (Pathologic) TSE -should not reach the brain
-without Sphingomylinase, Sphingomyelin is deposited in the brain
II. GLYCOLIPIDS
-important in Nerve Tissues and in the Cell Membrane
-widely distributed in every tissue of they body, particularly in Nervous tissue (Brain)
-occur particularly in outer leaflet of plasma membrane
-major glycolipids found in animal tissues are glycosphingolipids
A. Glycosphingolipids
-major glycolipids in animal tissues
-contain Ceramide + one or more Sugars
B. Galactosylceramide
-major glycosphingolipid of brain and other nervous tissue
-can be converted to Sulfogalactosylceramide (Sulfatide) present in Myelin
C. Cerebroside
-similar to Ceramide in Sphingolipids, but in C1, there is a sugar
D. Globoside
-similar to Cerebroside, but there are 2 or 3 sugars
E. Ganglioside
-similar to Globoside, but there are more than 3 sugars, complex oligosaccharide
-important because it is responsible for reaction of blood typing
-complex glycosphingolipids derived from Glucosylceramide with Sialic Acid
-present in nervous tissues in high concentrations
-presence of Sugar Derivation called Neuranunic Acid
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III. CHOLESTEROL
-falls under Sterols (contains a steroid nucleus)
-best known steroid because of its association with Atherosclerosis
-precursor of: Steroids (bile acids, Adrenocortical Hormones, Sex Hormones, D-Vitamins,
Glycosides, Sitosterols, Alkaloids)
-Cyclopentanoperhydro-phenantrene Ring
-3 Hexagonal rings, 1 Penatagonal ring
-18 Carbons
-cell membrane rigidity
-has a rigid Sterol Nucleus (man cant degrade cholesterol which is why it is converted to Bile Acid)
A. Ergosterol
-precursor of Vitamin D
B. Polyprenoids
-share the same parent compound as Cholesterol
-not steroids but related because they are synthesized like cholesterol
1. Ubiquinone -member of respiratory chain in motchondria
2. Dolichol -glycoprotein synthesis bt transferring carbohydrates to asparagines residues
**Isoprenoid Compounds -include Rubber, Camphor, Fat Soluble Vitamin A, D, E, K
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LECTURE 4: BIOENERGETICS
BIOENERGETICS -also known as Biochemical Thermodynamics
-study of the energy changes accompanying biochemical reactions
-explains how cell synthesis and utilizes energy for the maintenance of cellular homeostasis
-energy changes that are available to perform chemical and physical work keep us alive
**Concepts: Energy and the Thermodynamics Laws it follows
Forms of energy available / unavailable in the cell
Energy trapping system in the cell
I. LAWS OF THERMODYNAMICS
A. Law of Conservation of Energy
-the total energy in a system remains constant
-energy is neither created nor destroyed
-we consume and use energy stored in foods
-the source of energy is the Sun
-ex) Chemical Energy (Food)
Mechanical Energy (contraction of muscles)
Electrical Energy (neurons; trapping of energy)
Heat (Body Temperature)
B. Law of Entropy
-a system and its surroundings always proceed to a state of maximum disorder (maximum
entropy)
-the total entropy of a system must increase if a process is to occur spontaneously
-entropy is the randomness of a system (disordernes)
Gibbs Equation: G = H - TS S = Entropy / Randomness of a system
T = Absolute temperature
H = Enthalpy (Heat content of a compound)
G= Available Energy
**Gibbs Equation -applies to all reactions and processes
-Entropy effect is dependent on temperature (TS)
-if temperature is constant (human body), Enthalpy changes are negligible
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II. METABOLISM (combined Catabolic + Anabolic Processes)
A. Catabolism vs. Anabolism (types of metabolism) 1. Catabolism -Oxidation Reactions / Exergonic Reactions (generate free energy) -release of Electrons
1. Oxidation -release on electrons (e + H) -ex) Fe + Fe (+2) + e
FADH2 FAD + 2H(+) + 2es
2. Reduction -addition of electrons in hydrogen -reduction reaction are for synthesis
-ex) Synthesis of glucose from amino acid (not from lipids) NAD + 2H + 2es NADH + H(+)
III. FREE ENERGY (G) -the energy available for useful work; also known as chemical potential
-energy needed for the performance of work
-at equilibrium if G =0
A. Two Types of Reaction
1. Exergonic Reaction -has a negative free energy ( -G) -occurs spontaneously
-free energy is released -occurs with liberation of free energy (trapped by the cell) -termed as Catabolism Reactions
2. Endergonic Reaction -has a positive free energy ( +G)
-non spontaneous (reaction wont occur w/o energy) -needs addition of Energy -termed as Anabolism Reactions
-ex) Benedict’s Test (heat should be added: boiling) B. Coupled Reaction Systems
-endergonic reactions are often coupled with exergonic reactions -requirement: product of first reaction must be the substrate of the second reaction -have a common intermediate: A + C I B + D
-both can undergo completion
-net G is negative
A B Exergonic (-G) A B
B + C D Endergonic (+G)
B+C D C. Standard Free Energy Change (reactions occur in normal conditions) pH=7
C = 37 1 M
A + B C + D Keq = [C] [D] Products **Equilibrium Constant
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[A] [B] Reactants
IV. STEPS IN HARNESSING ENERGY FROM FOOD
-energy is extracted from food thru oxidation reactions, resulting to formation of CO2 and H2O
-occurs in four stages
-man gets energy needed to drive cellular reactions directly from the oxidation of foods
-man cannot use heat to drive cellular processes
A. Hydrolysis to Monomeric Units (Digestion)
-glucose, amino acids, fats are obtained respectively from carbohydrates, proteins, lipids
B. Conversion to the common intermediate: Acetyl CoA (Absorbtion)
-building blocks are degraded into Acetyl CoA (common intermediate)
-most of the energy contained in metabolic fuel is conserved in Chemical Bonds (electrons)
of Acetyl CoA
C. Degradation of the 2 Carbon Acetyl CoA in the TCA cycle in mitochondria (Redox Reaction) forming CO2
and Reducing Equivalent
-TCA cycle oxidizes Acetyl CoA to CO2
-electron pairs present in the Carbon-Carbon and Carbon-Hydrogen bonds are transferred to
electron carriers (NADH and FADH2)
**TCA Cycle -also known as Tricarboxylic Acid or Krebs Cycle
-localized in the Mitochondria
-Inner Mitochondrial Membrane has enzymes for trapping energy
-excess energy not trapped in chemical bonding during reaction is liberated
as heat
D. Coupling of the TCA cycle to Electron Transport Chain for Synthesis of ATP
-extraction of energy from food is the process of Oxidation Phosphorylation
-energy in electron pairs of NADH and FADH2 is released to Oxygen via Electron Transport
chain and is used for synthesis of ATP
1. The Electron Transport Chain (Energy Trapping System of the Cell)
-composed of specific sequence of Enzymes and their Coenzymes, including NAD
and FAD linked dehydrogenases
-electrons in NADH arise mainly from the Mitochondrial Oxidations
-all of the FADH2 arises from the Mitochonrial Oxidations
2. Synthesis of ATP (Trapping Energy)
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V. SYNTHESIS OF ATP (Trapping Energy)
-energy stored in ATP (Adenosine Triphosphate) is used to drive cellular processes
-through incorporation of ADP and Pi ATP (7 Kcal / mol)
A. Oxidative Phosphorylation
-Energy needed for Synthesizing Energy = 7.3 Kcal / mol
-flow of electrons from NADH releases sufficient energy to drive ATP synthesis
-Trapping of energy thru Oxidation of ATP in Electron Transport Chain
-food we eat is oxidized and releases free energy which is used to synthesize ATP
-more efficient because more ATP is synthesized
B. Substrate Level Phosphorylation
-synthesis of ATP through High Energy Compounds
-cleaving of bonds (should be higher than 7 Kcal / mol) releases Free Energy
-only one ATP is produced in one substrate level phosphorylation reaction
**High Energy Compounds
-broken and energy is released for ATP synthesis
-has groups that are Labile (easily broken)
1. Phosphoenol Pyruvate -enol has a double bond and alcohol metabolite of
phosphoenol pyruvic acid
2. 1,3-Bisphosphoglycerate -metabolite of glycolysis