Académique Documents
Professionnel Documents
Culture Documents
AMINO ACID
GLYCINE
ALANINE
VALINE
LEUCINE
ISOLEUCINE
PHENYLALANINE
TRYPTOPHAN
METHIONINE
PROLINE
DESCRIPTION
Aliphatic, No Chiral Center
Aliphatic
Aliphatic
Aliphatic
Aliphatic
Aromatic
Aromatic, Indole Group
Thioether Group, w/ Sulfur
Imino Acid
3-LETTER SYMBOL
GLY
ALA
VAL
LEU
ILE
PHE
TRP
MET
PRO
SERINE
THREONINE
CYSTEINE
ASPARAGINE
GLUTAMIN
TYROSINE
Alcohol
Alcohol
Thiol Group
Amide
Amide
Aromatic, Alcohol
SER
THR
CYS
ASN
GLN
TYR
S
T
C
N
Q
Y
ASPARTATE
GLUTAMATE
Carboxylate
Gamma-Carboxylate
ASP
GLU
D
E
LYSINE
ARGININE
HISTIDINE
Epsilon-Amino Group
Guanido Group
Aromatic, Imidazole Group
LYS
ARG
HIS
K
R
H
-Urea Synthesis
-Urea Synthesis
-Urea Synthesis
-Thyroid Hormone
-Neurotransmitter
-Collagen
-Collagen
-Thrombin, Fibrin
-Brain Tissues
-Brain Tissues
-Bacterial Cell Walls
-Bacterial Cell Walls
**Polar Environment
**Non-Polar Environ.
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
**Buffer
Monomeric
Multimeric
Homomeric
Heteromeric
BASIS
BOND TYPES
Covalent Peptide Bonds
Disulfide Bonds
SECONDARY
TERTIARY
H-Bonds
Electrostatic Reactions
Hydrophobic Effect
Vander Waals
QUARTERNARY
H-Bonds
Electrostatic Reactions
Hydrophobic Effect
Vander Waals
I. PRIMARY STRUCTURE
-sequence of amino acids Amino acid residues
-Nt AAAAAAAA- Ct
-made up of Covalent Peptide Bonds and Disulfide Bonds
- determines function and fate
II. SECONDARY STRUCTURE
-comes as a complex structure resulting from interactions of Amino Acid residues
-consider the types of Amino Acids (polar or non polar)
-depends on the charges in Amino Acids
-Supersecondary Structures
-secondary / tertiary
A. Alpha Helix
-Ampiphatic Right Hand Helices (R-groups face outward)
-Intramolecular H-Bonding (within molecule) and Vander Waals
-C=O of nth interact with N-H of n+4
-Pitch = 5.4 or 0.54nm
-every turn has 3.6 Residues of Amino Acids (36 per 10 turns)
Promote A-Helix
Ala A
Asn N
Cys C
Gln Q
His H
Leu L
Met M
Phe F
Trp W
Tyr Y
Val V
Destabilize A-Helix
Arg R
Glu E
Asp D
Gly G
Lys K
Ile
I
Ser S
Thr T
Terminate A-Helix
Pro P
Hyp.
-spring like because of Keratin Protein (to straighten hair, we wet it)
-hair does not dissolve in water because Alpha-HeliX is Ampiphatic
-because of Hydrophobic Amino Acids which go away from water
-in rebonding, they add a reducing agent to break disulfide bonds, then they add
an oxidizing agent to arrange disulfide bonds
**Ramachadran Plot
B. Beta Sheet
-Stabilized by Intermolecular H-Bonding between polypeptide chains
-2 residue repeat distance = 7.0A or 0.70nm
-usually found in long proteins
-requires 2-strands to form B-Sheet
-can be Intermolecular (2 strands) of Intramolecular (w/in 1 strand)
-Glycine can squeeze into bends
-two types: Parallel (NC and NC) and Anti-Parallel (NC and CN)
-ex) Silk - stretching silk will break it because it is already in its fully extended form (Beta-sheet)
1. Domain
-two or more distinct modules
2. Motifs
-recurring substructures
-includes the B-A-B Motif + Hairpin Loop Motif
-B-A-B Motif: beta sheet Alpha Helix beta sheet (contains a parallel beta sheet)
-Hairpin Loop Motif: 2 beta sheets not facing the same direction (anti parallel)
C. Other Secondary Structures
1. Bends
-joining of two secondary structures (short)
2. Loops/Turns
-forms Supersecondary Structures
-has an irregular conformation
-gives flexibility to the protein
-found in Helix Loop Helix Motifs (DNA) and Epitopes (Antibodies)
Motifs
- repeat structure which occurs regularly at intervals
Epitopes
- loops on surface which are readily accessible sites
3. Random Coil -irregular structures
III. TERTIARY STRUCTURES
-3-D Arrangement of proteins which is a combination of several secondary structures
-may be Globular / Fibrous
-Surface of protein contains polar amino acids; Interior of protein contains non-polar amino acids
-stabilized by non-covalent interactions (Hydrophobic Interactions, Electrostatic / Ionic Bonding, Van der Waals
or Hydrogen Bonding)
-includes Domains (Supersecondary Structures) to perform a particular function
B-A-B Motif: beta sheet Alpha Helix beta sheet (contains a parallel beta sheet)
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
Waals, Hydrogen Bonding)
**Denaturation of Proteins
**Aggregates
-unfolding of proteins
-proteins which have failed to refold spontaneously
C. Molecular Modeling
IV. DISEASES RELATED TO PROTEIN FOLDING
A. Alzheimers 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. Madcows 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
-Hydrophobic R-Groups are exposed (insoluble)
-Beta Sheet
V. EXAMPLES OF PROTEINS
A. Alpha Keratin
-found in Hair, Wool, Feathers, Nails, Claws, Scale, Horns, Hooves, etc
-Right handed Alpha-Helix
-Rich in F, I, V, M, A
-cross links contributed by Disulfide bonds (cysteine)
B. Collagen
-fibrous protein found in Connective Tissues, Tendons, Cartilage, Cornea (most abundant)
-functional collagen is a triple helix (right handed)
-Left handed twist is formed by the triple helix
-Unique collagen helix with unusual angles
-Helix is stabilized by Steric Repulsions
-3.3 Amino acids per turn
-Glycine is present in every third residue
-Hydoxylysine involved in H-bonds
-constant composition: G, A, P, Hydroxyproline
-damaged in diabetic people (high glucose level)
-fragile collagen may result to scurvy: bleeding gums, skin discoloration (caused by
Vitamin C deficiency)
LECTURE 2: CARBOHYDRATES
CARBOHYDRATES
-Carbohydrates may be attached to proteins or to lipids in the membrane
I. FUNCTIONS OF CARBOHYDRATES
Energy: Glucose is the main fuel of the cell
Storage: Starch (plants) and Glycogen (animals)
Structural: Cellulose / Chitin; Hemicellulose; Agar; Spectin
Cell to Cell Signalling
Antigen / Markers
Fillers for Drugs
Proteoglycans / Mucopolysaccharides
Cell Membrane Component (Glycolipid, Glycoroteins)
Antibiotics
II. REQUIREMENTS TO BE CONSIDERED A CARBOHYDRATE
A. Must have a Carbonyl Group ( --C=O)
o Ketone (Ketose)
o Aldehyde (Aldose)
**AnUmeric Carbon
D-Glucose
D-Fructose
WHERE FOUND
BIOCHEMICAL IMPORTANCE
HEXOSES
Sugar of the body carried by blood and used by tissues
D-Galactose
Hydrolysis of Lactose
D-Mannose
D-Ribose
Nucleic Acids
D-Ribulose
D-Arabinose
D-Xylose
D-Lyxose
D-Xylulose
PENTOSES
Structural elements of nucleic acids and coenzymes (ATP,
NAD, NADP)--Ribose Phosphate is an intermediate to pentose phosphate
pathway
Ribulose Phosphate is an intermediate in pentose phosphate
pathway
Constituent of Glycoproteins
Constituent of Glycoproteins
Constituent of a lyxoflavin isolated from human heart muscle
**Glucose
10
**D-Glucosamine
**D-Galactosamine
II. DISACCHARIDES
-condensation products of two monosaccharide units
-important disaccharides include Maltose, Sucrose, Lactose
-Oligosaccharides: condensation of 2-10 monosaccharides -ex) Maltotriose
**Glycosidic Bonds
SUGAR
Maltose
Glucose + Glucose
SOURCE
Digestion by amylase or hydrolysis of
starch
CLINICAL SIGNIFICANCE
Lactose
Galactose + Glucose
Sucrose
Glucose + Fructose
Trehalose
**Maltose
**Isomaltose
**Lactose
**Sucrose
11
III. POLYSACCHARIDES
-condensation of more than ten monosaccharide units which may be linear or branched polymers
-may be classified as Hexosans or Pentosans
-for storage and structural functions
A. Homopolysaccharides (same monomer units)
1. Starches
3. Dextrins
4. Inulin
5. Cellulose
6. Chitin
2. Glycoproteins
12
**Neuraminic Acid
CHARACTERISTICS OF CHO
I. STRUCTURES OF CARBOHYDRATES
A. Three Types of Representations Used:
1. Fischer Projection
-two dimensional perspective
2. Haworth Projection
-cyclic sugars
-may be a Pyranose (6 membered) or Furanose (5 membered)
-Amylene Bridge connects the Functional Group and Alcohol
**Hemiacetal
**Hemiketal
3. Chair Configuration
B. Isomerism in Sugars
-Number of Isomers = 2n; where n= # of chiral centers
-ex) in D-Glucose, there are 4 chiral centers, which means, D-glucose has 16 sterioisomers
** (1) Enantiomer: mirror image
** (14) Diasterioisomers: not sterioisomers nor mirror image
1. Enantiomer: Mirror Image
-either D or L form OR may also be (+) or (-)
-D/L and +/- are independent of each other
-most of the carbohydrates in mammals are D-Sugars
-depends on the Penultimate Carbon (last chiral center / 2 nd to the last Carbon)
**D-Sugar
**L-Sugar
**Dextrorotatory (+)
**Levorotatory ( - )
**Beta
3. Epimers
-sugars that differ on orientation of OH in only one carbon (except anomeric carbon)
-ex)
Mannose and Glucose (C-2 Epimers)
Glucose and Galactose (C-4 Epimers)
4. Aldose-Ketose Isomerism
-ex) Fructose has same molecular formula as glucose but differs in its structural formula, since there is a
potential keto-group in Fructose and a potential aldehyde group in Glucose
13
2. Aldonic Acid
3. Uronic Acid
**N-Glycosidic Bond
C. Deoxysugars
-hydroxy group has been replaced by a hydrogen
-ex)
Deoxyribose in DNA
Deoxy Sugar L-Fucose occurs in Glycoproteins
2-Deoxyglucose used as an inhibitor of glucose metabolism
D. Amino Sugars
-Amino groups replaces an OH group
-ex)
D-Glucosamine -constituent of Hyaluronic Acid
D-Galactosamine (Chondrosamine) -a constituent of Chondroitin
D-Mannosamine
Antibiotics
14
15
LECTURE 3: LIPIDS
LIPIDS
-diverse structures
-includes fats, oils, steroids, waxes, and related compounds
-two common properties of all Lipids:
1. Insoluble in water
2. Soluble in non-polar solvents (such as ether and chloroform)
-stored in adipose tissue
I. FUNCTIONS OF LIPIDS:
High energy value
Fat soluble vitamins and essential fatty acids
Serves as thermal insulator in adipose tissue in the subcutaneous insulators
Act as electrical insulators, allowing depolarization waves (along myelinated nerves)
Important constituent in membrane and mitochondria (lipoproteins)
Transporting lipid in the blood
Protective padding and insulation of vital organs
II. FATTY ACIDS
-aliphatic carboxylic acids; building blocks
-occur mainly as esters in natural fats and oils but occur in the unesterified form as free fatty acids
-free fatty acids is a transport form found in the Plasma
-usually straight-chain derivatives containing an EVEN number of carbon atoms
-ampiphatic (with hydrophilic and hydrophobic ends)
**Nomenclature of Fatty Acids
1. Saturated Acids
-end with anoic
-ex) Octanoic Acid
2. Unsaturated Acids
16
# C
2
Propionic Acid
Butyric Acid
Valeric Acid
Caproic Acid
Lauric Acid
3
4
5
6
12
Myristic Acid
Palmitic Acid
Stearic Acid
Arachidic Acid
Behenic Acid
Lignoceric Acid
14
16
18
20
22
24
DESCRIPTION
End product of carbohydrate fermentation by rumen
microorganisms
End product of carbohydrate fermentation by rumen organisms
In certain fats in small amounts (butter). End product of
carbohydrate fermentation by rumen organisms
Spermaceti, Cinnamon, Palm Kernel, Coconut Oils, Butter,
Laurels
Nutmeg, Palm Kernel, Coconut Oils, Butter
Common in all animal and plant fats
2. Polyunsaturated
3. Eicosanoids
Thromboxanes
Prostacyclins
b. Leukotrienes (LTs)
c. Lipoxins (LXs)
17
18
9. Hormones
LIPID CLASSIFICATION
I. PHOSPHOLIPIDS
-main lipid constituents of membrane
-derivatives of Phosphatidic Acids
**Phosphatidic Acid
A. Phosphoglycerides / Glycerophospholipids
-depend on structures attached to Phosphatidic Acid
1. Phosphatidyl Cholines (Lecithin)
-Phosphoacylglycerols containing Choline
-most abundant phospholipids of the cell membrane
**Choline
19
B. Sphingolipids
-parent structure is an alcohol called Sphingosine
**Sphingosine
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
20
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
**Isoprenoid Compounds
21
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:
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)
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
**Gibbs Equation
22
AB
Exergonic (-G)
Endergonic (+G)
B+C
C. Standard Free Energy Change (reactions occur in normal conditions)
pH=7
C = 37
1 M
A+BC+D
Products
**Equilibrium Constant
23
24
2. 1,3-Bisphosphoglycerate
-metabolite of glycolysis
3. Creatine Phosphate
-skeletal muscles
-Creatine Creatinine
4. Pyrophosphate
**Low Energy Compounds
1. Glucose 1-Phosphate
2. Fructose 6-Phosphate
3. AMP
4. Glucose 6-Phosphate
5. Glycerol 3-Phosphate
**ATP (Adenosine Triphosphate)
-ATP can be cleaved in two ways:
Cleaved to AMP + PPi 2 Pi
Pi + ADP
25