BIOCHEMISTRY

BIOCHEMISTRY = Chemistry of life = Study of life in the molecular level = It is concerned with the biological molecules of living organisms; its structure, properties and functions. IMPORTANCE OF BIOCHEMISTRY Biochemical studies lead us to fundamental understanding of life. All of us have natural curiosities on how our bodies work. What will happen to the food we have eaten could be answered through this course, for example. BIOMOLECULES = living organisms are composed of thousands of different kinds of inorganic and organic molecules.

Five Major Complex Biomolecules 1. DNA 2. RNA 3. CHON 4. CHO 5. LIPIDS IMPORTANT FUNCTIONAL GROUPS IN BIOMOLECULES Alcohol OH Hydroxyl Aldehydes CHO Carbonyl Ketone C=O Carbonyl Acids COOH Carboxyl Amines NH2 Amino Amides CONH2 Amide Thiols SH Thiol Ester COOR Ester Alkene C=C Double bond Alkane C-C Single bond

CHIEF COMPONENTS OF THE HUMAN BODY 1. Protein = 17 % 2. Water = 61.6% 3. Fats = 13.8 % 4. Minerals and Vitamins = 6 % 5. Carbohydrates = 1.5 % Elementary composition of the human body 1. Carbon 2. Oxygen 3. Hydrogen 4. Nitrogen Phosphate is a component of the nucleic acids Calcium is important also in biologic processes Other elements include: K Na Cl Mg Fe Mn I S

THE CELL
It is the structural unit of living systems, it is the fundamental unit of biologic activity It is the building blocks of life PARTS OF THE CELL 1. NUCLEUS is an organelle inside the cell that directs the activity inside it. = it holds the DNA or Deoxyribonucleic acid = it is enclosed in a double membrane and communicates with the surrounding cytosol = site of chromosomes = site of DNA directed RNA synthesis or transcription 2. Nucleolus it is the prominent structure in the nucleus

= it produces ribosomes 3. Nuclear Envelope is the double membrane surrounding the nucleus of a cell 4. Nuclear Membrane controls the movement of materials in or out of nucleus = intercellular adhesion and communication 5. Cytoplasm is the collective term for the cytosol plus the organelle suspended within the cytosol 6. Golgi Body is a membrane-bound structure with a single membrane = stacks of sacs that package and move proteins around in the cell = package and export proteins = intracellular sorting of proteins = Glycosylation and Sulfation reaction occurs 7. Cell Membrane is a protective layer that covers the cells surface = controls the movement of materials in or out of cell = made more complex by the presence of numerous proteins that are crucial to cell activity = intercellular adhesion and communication = Na K ATPase as a marker 8. Mitochondria is the power center of the cell = it releases energy in the cell = produces ATP using energy stored in food molecules = breaks down sugar molecules to release energy = Krebs cycle is formed = glutamic dehydrogenase as marker 9. Ribosomes contains packets of RNA and CHON = it has large subunit and small subunit = messenger RNA or mRNA from the cell nucleus is moved systematically = transfer RNA or tRNA adds A.A molecules to the lengthening CHON chain = site of protein synthesis 10. Endoplasmic reticulum it is a folded membrane that moves material in the cell = network of tubes or membranes = responsible for moving proteins and other CHO to the Golgi body = it is the site of synthesis of various lipids = oxidation of many xenobiotics like cytochrome P- 450 11. Rough Endoplasmic reticulum or RER is an iterconnecting stacks of disc-like sacs = appears pebbled by electron microscopy due to the presence of numerous ribosomes on its surface

12. Smooth Endoplasmic reticulum or SER = appears smooth by electron microscopy = being tubular than disc like = synthesis of lipids = it is a small sac that moves material in and out of the cell = stores food, water, metabolic, and toxic wastes 13. Plasma membrane = Encloses the contents of all living cells = Regulate the passage of molecules in and out of the cells COMPOSITION OF THE CELL ORGANIC 10- 25% -BIOMOLECULES OTHERS- COENZYMES INORGANIC about 1% -Water 70-90 - Ions: abundant Na, K, Ca, Mg Trace Ions: Zn, Fe, Cu, Mn, Co, Sn, Cr ABUNDANT IONS: 1. Sodium - most abundant in the extracellular ion. - activates ATPase which leads to ADP formation - causes water retention 2 . Potassium - most abundant in the intracellular ion - required by enzymes like ATPase, pyruvate kinase, phosphatases - low level can lead to sudden death 3 . Calcium - required during blood clotting for the conversion of prothrombin to thrombin. Calmodulin - calcium carrier protein which when bound can perform : 1. phosphorylation of various proteins 2. calcium metabolism

3. cyclic nucleotide catabolism 4. glycogen metabolism 4. Magnesium - present mainly in RBC - activates, transphosphorylases, enolases, peptidases, etc. TRACE IONS 1. Iron - 70 % in hemoglobin - it is also found in myoglobin cytochrome peroxidises, catalases, oxidases and in iron sulfur proteins. 2. Zinc - 90% of all enzymes require zinc. Deficiency leads to: 1. growth retardation 2. low RBC 3. dermatitis 4. poor wound healing 5. impaired immune response 3. Iodine contained in the thyroid hormone 4. Chromium helps maintain normal growth level by interacting with insulin receptors. 5. Mn enzyme cofactor of histidase, amino peptidase 6. Copper required by variety of enzymes: cytochrome oxidase, ascorbic acid oxidase, tyrosinase, uricase 7. Cobalt found in cyanocobalamin coenzyme 8. Sn stabilizes tertiary protein structure. PROTEINS Are the most abundant substances in nearly all cells. Comes from the Greek word proteios, which means of first importance. It is naturally occurring, unbranched polymer in which the monomer units are amino acids. It contains the element: Carbon Hydrogen Oxygen Nitrogen

 Sulfur

AMINO ACIDS: THE BUILDING BLOCKS FOR PROTEINS It is an organic compound that contains both an amino (-NH2) group and a carboxyl (COOH) group. The amino acids found in proteins are always -amino acids. GENERAL FORMULA OF AMINO ACID H | H2N - C COOH | R Amino Acids are Grouped According to Side Chain Polarity Nonpolar amino acids Polar amino acids Polar acidic amino acids Polar basic amino acids

CLASSIFICATION OF AMINO ACIDS Capacity to Interact with Water 1 Non polar amino acids -Their R-groups do not carry charges and they interact poorly with water or hydrophobic. EX .glycine, alanine, valine, leucine, isoleucine, phenylalanine, trytophan, methionine, proline 2. Polar amino acids -Contain functional groups capable of forming hydrogen bonds which can interact with water or hydrophilic. EX . Serine, theonine, tyrosine, asparagines, glutamine 3. Acidic amino acids -Contains carboxylate side chains such as aspartic acid and glutamic acid. 4.Basic amino acids -They form ionic bonds with acidic amino acids.

EX. Lysine, Arganine, Hisitidine II-According to R-group ALIPHATIC AMINO ACIDS EX. Glycine, Alinine, Valine, Leucine, Isoleucine AROMATIC AMINO ACIDS EX. Phenylalanine, Tyrosine, Trytophan HYDROXY AMINO ACIDS EX. Serine, Theonine ACIDIC AMINO ACIDS EX. Aspartic acid, Glutamic acid BASIC AMINO ACIDS EX. Lysine, Arginine, Histidine SULFUR AMINO ACIDS EX. Cysteine, Methionine STRUCTURE OF BENZENE RING

NONPOLAR AMINO ACID

POLAR SIDE CHAINS

ACIDIC SIDE CHAINS

BASIC SIDE CHAINS

CLASSIFICATION OF ACID ACCORDING TO NUTRITION VALUE Essential amino acid Arginine Histidine Isoleucine Valine Leucine Lysine Methionine Phenylalanine Threonine Tryptophan CLINICAL SIGNIFICANCE: Phenylketonuria = F is converted into Tyrosine by Phenylalanine hydroxylase, Tyrosine becomes essential and F builds up, leading to excess phenylketones in urine Findings: MR, growth retardation, fair skin, eczema, musty body odor Tx: decrease F and increase tyrosine in diet Screened for at birth or NBS Albinism = congenital deficiency of either of the ff: 1. Tyrosinase = inability to synthesize melanin from tyrosine = autosomal recessive Lack of melanin results in increase risk of skin cancer 2 . Defective tyrosine transporters = decrease amounts of tyrosine and thus melanin Maple syrup urine disease = blocked degradation of branched amino acid, Ile, Val, Leu, due to decrease a ketoacid dehydrogenase, increases a ketoacids in the blood especially Leu Causes CNS defects, MR and death Urine smells like maple syrup Non essential amino acids Glycine Alanine Cysteine Tyrosine Asparagines Glutamic acid Serine Aspartic acid Proline

Abbreviations and symbols for the commonly occurring AA Unique first letter Cysteine= Cys= C Histidine = His= H Isoleucine = Ile = I Methionine = Met = M Serine = Ser = S Valine = Val = V According to priority Alanine = Ala = A Glycine = Gly = G Leucine = Leu = L Proline = Pro = P

Similar sounding names: Arginine = Arg = R Asparagine = Asn = N Aspartate = Asp = D Glutamate = Glu = E Glutamine = Gln = Q Phenylalanine = Phe = F Tyrosine = Tyr = Y Tryptophan = Trp = W Optical properties of amino acids a carbon of AA is attached to 4 different chemical groups and is chiral or optically active Glycine is an exception because its carbon has 2 H substituents and is inactive designated D and L for the mirror imaged AA the 2 forms in each pair are termed stereoisomers, optical isomers or enantiomers Optical isomers of Alanine COOH I H3N -C- H I CH3 L- Alanine HOOC I H- C- NH3 I H3C D- Alanine

 Glycine

H I H3N - C - COOH I H

ACID BASE PROPERTIES OF AMINO ACIDS In neutral solution, carboxyl groups have a tendency to lose protons (H+), producing a negatively charged species In neutral solution the amino groups have the tendency to accept protons (H+) producing a positively charged species The COOH group of an amino acid donates a proton to the amino acid Such molecule is known as the zwitterion

Zwitterion It is a molecule that has a positive charge on one atom and negative charge on another atom but which has no net charge. Zwitterion form: H | H3N+ -C COO | R Isoelectric point Isoelectric point is the pH at which an amino acid solution has no net charges because an equal number of positive and negative charges present.

pH and Buffers AA contain weakly acidic COOH group or weakly NH3 group therefore they can act as BUFFERS Buffers are the solutions that resists change in pH ff the addition of an acid or base Quantitative relationship between the concentration of weak acid, HA and its base A is described by Henderson Hasselbach equation Henderson Hasselbach equation

Where: pka is the negative log dissociation constant [A-] = molar concentration of a conjugate base [HA] = molar concentration of a undissociated weak acid (M) Calculate the pH of a buffer solution made from 0.20 M HC2H3O2 and 0.50 M C2H3O2- that has an acid dissociation constant for HC2H3O2 of 1.8 x 10-5. pH = pKa + log ([A-]/[HA]) pH = pKa + log ([C2H3O2-] / [HC2H3O2]) pH = -log (1.8 x 10-5) + log (0.50 M / 0.20 M) pH = -log (1.8 x 10-5) + log (2.5) pH = 4.7 + 0.40 pH = 5.1 STRUCTURE OF PROTEINS Primary structure PEPTIDES It is an unbranched chain of amino acids, each are joined to the next by a peptide bond.

 Peptides are further classified into dipeptides tripeptides polypeptides Amino acid residue is the portion of an amino acid structure that remains after the release of water. Peptide Nomenclature IUPAC Rules for naming small peptides are as follows: The C-terminal amino acid residue keeps it full amino acid name. 2. All of the other amino acid residues have names that end in yl. The yl suffix replaces the ine or ic acid ending of the amino acid name, for tryptophan (tryptophyl), cysteine (cysteinyl), glutamine (glutaminyl), and asparagine (asparginyl). 3. The amino acid naming sequence begins at the N-terminal amino acid residue Peptide bond = proteins are joined by peptide bonds which are amide linkages between the a carboxyl group of one amino acid Characteristics of the peptide bond: partial double bond character rigid planar trans bond instead of cis PRIMARY STRUCTURE

Secondary structure Is the arrangement of H bonds between the peptide nitrogens and the peptide carbonyl oxygens of different AA alpha Helix = most common = spiral structure with the side chains of the component AA extending outward from the central axis to avoid interfering sterically with each other = common coil is right handed alpha helix Secondary structure Alpha helix

= stabilized by hydrogen bonds = each turn contains 3.6 amino acids Examples are: = a keratin from hair and nails = Myoglobin Amino acids that disrupts a Helix Proline Glutamate, Aspartate, Histidine, Lysine or Arginine Tryptophan, Valine or Isoleucine B sheet = peptide bond components are involved in hydrogen bonding = B sheets appear pleated = composed of of 2 or more peptide chains = parallel and antiparallel sheets = interchain bonds

Beta Helix

B bends or reverse turns = reverse the direction of a polypeptide chain, helping it form a compact, globular shape = usually found on the surface of protein molecules = connect successive strands of antiparallel B sheets = generally composed of 4 AA Tertiary Structure of Proteins The primary structure of polypeptide chain determines its Tertiary structure Tertiary refers both to the folding of domains, the basic units of structure and function and the final arrangement of domains in the peptide = Hydrophobic side chains are buried in the interior = Hydropilic groups are found on the surface

Tertiary structure

Domains = fundamental functional and three dimensional structural units of polypeptide Interactions stabilizing tertiary structure: Disulfide bonds is a covalent linkage formed from the sulfhydryl group, SH, of 2 cysteine residues to produce cysteine residue = contributes to the stability of the three dimensional shape of the protein molecule Hydrophobic interactions = AA with nonpolar side chains tend to be located in the interior of the polypeptide molecule, AA with polar or charged side chains tend to be located on the surface of the molecule in contact with polar solvent Hydrogen bonds its formation between polar groups on the surface of proteins and the aqueous solvent enhances the solubility of the protein Ionic interactions = negatively charged groups such as the COO in the side chain of aspartate or glutamate, can interact with positively charged groups such as the amino group,NH3 in the side chain of lysine Protein Folding = interactions between the side chains of AA determine how a long polypeptide chain folds into the intricate three dimensional shape of the functional protein = occurs within cell in seconds to minutes Steps in protein folding Formation of secondary structures Formation of domains

 Formation of final protein monomer = Chaperones or heat shock proteins are required for proper folding of many species of proteins = they interact with polypeptide at various stages during folding process Quaternary Structure of Proteins 2 or more polypeptide chains that may be structurally identical or totally unrelated if theres 1 subunit = monomeric if there are 2 subunits = dimeric three subunits = trimeric several subunits = multimeric Denaturation of protein results in the unfolding and disorganization of the proteins 2 and 3 structure Denaturing agents include heat, organic solvents, strong acids or bases, detergents and ions of heavy metals such as lead and mercury Quaternary Protein structure

Protein denaturation Refers to unfolding and rearrangement of the secondary and tertiary protein structure without breaking the peptide bond. A protein that is denatured loses its biologic activity.

 It is the partial or complete disorganization of a proteins characteristic three dimensional shape as a result of disruption of its secondary, tertiary and quarternary structural interactions. The result of denaturation is the loss of biochemical activity. Protein Misfolding = results from processes that results from improperly folded molecules which are usually tagged and degraded by the cell Clinical significance: Amyloidoses caused by accumulation of aggregating proteins, consisting B pleated sheets, called the AMYLOIDS, has been implicated in many degenerating diseases particularly in the neurodegenerative disorder, Alzheimer disease = the amyloid plaque in AD is Amyloid beta Prion disease or PrP has been implicated as the causative agent of bovine spongiform encephalopathy I cattle popularly called mad cow disease = infection protein is prion protein, infectious and highly resistant to degradation and when infectious, tends to form insoluble aggregates of fibrils similar to the amyloid BIOCHEMICALLY IMPORTANT SMALL PEPTIDES 1. Small peptides hormones - Oxytocin - Vasopressin 2. Small peptide neurotransmitters - Enkephalins - met-enkephalins - leu-enkephalins 3. Small peptide antioxidants - Glutathione Qualitative tests for amino acids
Reaction Ninhydrin Reactive group Alpha-amino group Product Blue-violet complex

Folins

Sodium 1,2-naphthaquinone 4sulfonate Phenol group of tyrosine Nitration of benzene Presence of tryptophan (indolering) SH of cysteine Cystine/cystein Guanidine in arginine Arginine

Deep red color

Millons Xanthoproteic Hopkinscole

Old rose complex/pink to red ppt. Yellow ppt. Reddish violet ring

Reduced sulfur or Pb acetate Sulivan cyctine Sakagucci Diacetyl

Black ppt, PbS Red Red orange Pink color with green fluorescence

Properties of simple proteins

TYPES OF PROTEIN Albumins Globulins SOLUBILITY Soluble in water and salt solutions Slightly soluble in water, soluble in salt solutions Insoluble in all neutral solvents and in dilute acid and alkali Soluble in salts solutions, insolute in every dilute NH4OH COAGULATED BY HEAT Yes Yes EXAMPLES Egg albumin, serum albumin, lactalbumin Serum globulin, lactoglubin, vegetable globulin Keratin in hair, nails, Feathers, collagen

Albuminoids

No

Histones

No

Nucleohistones in thymus gland, globin in hemoglobin

TYPES OF CONJUGATED PROTEINS

Class Prosthetic group Heme unit Specific examples Functions of examples

Hemoprotein

Hemoglobin Myoglobin

Carrier of O2 in blood Oxygen binder in muscles Lipid Carrier Lipid carrier

Lipoproteins

Lipid

Low density Lipoprotein (LDL) High-density Lipoprotein ( HDL)

Glycoprotein

Carbohydrates

Gamma globulin Mucin Interferon

Antibody Lubricant in mucous secretion Antiviral protection

Phosphoproteins

Phosphate group

Glycogen Phophorylase Ribosomes Viruses

Enzyme in glycogen phoisphorylation Site for protein synthesis in cells Self-replicating infections

Nucleoproteins

Nucleic acid

Classification of protein based on shape Fibrous protein - A protein whose molecule is elongated shape with one dimension. - Generally water insoluble - Usually have single type of secondary structure - It provides support and external protection - Most abundant proteins in human body - Cannot be readily denatured Globular proteins - A protein whose molecule have peptide chains that are folded into spherical orglobular shapes - Water soluble - Contain several types of secondary structure - Involved in metabolic chemistry, performing functions such as: catalysis, transport and regulation - Denature more readily Some common fibrous and globular proteins Fibrous proteins -- serve as structural functions in the body -- abundant in nature -- it is major constituent of hair, feather, wool, fingernails and toenails, claws, scales, horns, turtle shells, quills, and hooves, skin, connective tissue, BV walls, sclera and cornea Collagen- the most abundant of all proteins in humans (30% of total body protein) - it is the major structural material in tendons, ligaments, blood vessels and skin - it is also the organic component of bones and teeth. Elastin - found in blood vessels and ligaments Myosin - found in muscle tissue

Fibrin - found in blood clots Collagen

Type 1 11 111 1V V11 1X X11 Tissue Distribution FIBRIL FORMING SKIN, BONE, TENDON, CORNEA CARTILAGE, INTERVERTEBRAL DISK, VITREOUS BODY BV, FETAL SKIN NETWORK FORMING BASEMENT MEMBRANE BENEATH STRATIFIED SQUAMOUS EPITHELIA FIBRIL ASSOCIATED CARTILAGE TENDON, LIGAMENTS, SOME OTHER TISSUES

Collagen diseases Ehlers-Danlos syndrome or EDS = defect in the metabolism of fibrillar collagen molecules = Type 111 collagen is most frequently affected resulting in BV instability = Type 1 defect results in stretchy skin and loose joints SSx: Hyperextensible skin, tendency to bleed, hypermobile joints Osteogenesis Imperfecta is known as Brittle Bone Disease, an inherited disorder distinguished by bones that easily bend and fracture leads to humped back appearance; blue sclerae due to transluscency of the connective tissue over the choroid, hearing loss and dental imperfection Elastin a connective tissue protein with rubber like properties; composed of elastin and glycoprotein found in the lungs, the walls of large arteries and elastic ligaments =rich in proline and lysine

Clinical significance: Marfans syndrome is caused by a defect in fibrillin characterized by lens dislocation, aortic dissection and joint hyperflexibility Globular proteins 1. Insulin - Regulatory hormone for controlling glucose metabolism 2. Myogoblin - Oxygen storage molecule in muscles 3. Hemogoblin - Transport oxygen from the lungs to tissue 4. Transferrin - Involved in iron transport in blood 5. Immunoglobulin a. Involved in immune system responses

Hemoglobin and Myoglobin = 2 most abundant hemeproteins in human

+Hgb= T for taut form = low affinity for O2 = R for relaxed form = high affinity for O2 = found exclusively in RBC and functions to transport O2 from the lungs to the capillaries of the tissues Hemoglobinopathies

1. Sicke cell disease = genetic disorder of the blood caused by alteration in the globin chain characterized by lifelong episodes of crises, chronic hemolytic anemia and increased susceptibility to infections 2. Thalassemias = hereditary hemolytic diseases in which an imbalance occurs in the synthesis of globin; RBC dont mature which lead to severe anemia which can be life threatening
Type of protein Structural Example Collagen Keratin Contractile Myosin Actin Storage Ferritin In storage of iron needed to make Hgb In carrying O2 In carrying fatty acids Use In structure of connective tissue In structure of hair and nails In muscle contraction

Transport

Hgb Serum Albumin

Hormones Enzymes Protective

Insulin Pepsin Gamma globulin Fibrinogen

In metabolism of CHO In digestion of CHONs In Ab formation In blood clotting

Toxins

Venoms

Poisons

Proteins are precipitated by: 1. Acids = Inorganic precipitants are: HNO3 and HClO4 = Organic precipitants are: C2HCl3O2 ,H2MoO4, C6H3N3O7, C76H56O46 Picric acid is used in the tx of burns because it produces an astringent effect on the tissue Tannic acid is used to relieve diarrhea; also incorporated in an ointment for burns, producing protective crust of protein tannate over delicate area Sulfosalicylic acid is used to detect proteins quantitatively and determine them in urine and body fluids = acids which precipitate the proteins are sometimes termed alkaloidal reagents = Roberts test: reagent is HNO3 which results to white precipitate = Hellers test: reagent is HNO3 which results white precipitate turning yellow 2 Salts of heavy metals (Hg, Ag, Pb) the metals unite with the COOH, thus forming proteinates 3 Neutral salts ( Na2SO4, NaCl) used to precipitate proteins or salt out proteins precipitation may be due to dehydration of molecular aggregates in solutions

Color reactions protein Biuret test

 Specific color test for proteins Reagent: NaOH, Cu SO4 Result: violet color Indication: presence of peptide linkage or other closely related group: 4 Alcohol
Denaturing agent

the addition of alcohol to protein has two effects depending on the concentration of the solution 4.1 if the solution is diluted 4.2 at high alcohol concentration
Mode of action

Heat

Disrupts hydrogen bonds by making molecules vibrate too violently; produces coagulation as in the frying of an egg Causes violently of molecules that disrupt hydrogen bond Operates very similarly to the action of heat Causes molecules in globular shapes to extend to longer lengths which then entangle. Affects R group ineractions Interfere with R group interactions because these solvents also can form hydrogen bonds; quickly denature proteins in bacteria, killing them (disinfectant action of 70% ethanol)

Microwave radiation Ultraviolet radiation Violent whipping or shaking Detergent Organic solvents (e.g. alcohol, 2 propanonol, acetone)

Strong acids and bases

Disrupt hydrogen bonds and salt bridges; prolonged action leads to actual hydrolosis of peptide bonds

Salts of heavy metals

Metal ions combine with -SH groups and form poisonous salts