BIOCHEMISTRY

Lesson 1
Cell Structures and Its Functions
CYTOSOL o Intracellular fluid where organelles and cell inclusions are suspended.
NUCLEUS o Large spherical and oval shape
o Contains genetic material of the cell
o Site of DNA and RNA biosynthesis
RIBOSOMES o Consists of two unequal subunits
o Composed of proteins and RNA
o Site of protein synthesis
ENDOPLASMIC RETICULUM o Network of membrane enclosed channels continuous with the nuclear pore
o Processes and transports proteins from one site to another
o Contains enzymes responsible for detoxifying substances that enters the cell
GOLGI COMPLEX o Membranous vesicles stacked upon one another with expanded bulges at their sides
o Sorts and transports molecules for export into the plasma membrane or other cells
LYSOSOME o Contains hydrolytic digestive enzymes aimed for intracellular digestion
*hydrolytic digestive enzymes are responsible for detoxifying chemicals
PEROXISOMES o Smaller than lysosomes
o Contains oxidative enzymes
MITOCHONDRION o Site of cellular respiration
*PARTS: cristae and matrix
SECRETORY VESICLES o Contains secretory products of the cell
CELL WALL o Supporting structure surrounding plant cells
o Made up of cellulose
o Causes rigidity of plant cells
*Ruminant animals are herbivores that can digest cellulose
CHLOROPLASTS o A type of plastid containing chlorophyll, the pigment responsible for photosynthesis
VACUOLE o Found in the cytoplasm serving as a reservoir for the food and waste products
Structures of the Standard Amino Acids
ALKYL Glycine (Gly, G)
Alanine (Ala, A)
Valine (Val, V)
Isoleucine (Ile, I)
Leucine (Leu, L)
Proline (Pro, P)
SULFUR CONTAINING Cysteine (Cys, C)
Methionine (Met, M)
ALCOHOLS Serine (Ser, S)
Threonine (Thr, T)
ACIDS Aspartic Acid (Asp, D)
Glutamic Acid (Glu, E)
BASES Arginine (Arg, R)
Histidine (His, H)
Lysine (Lys, K)
AROMATIC Tyrosine (Tyr,Y)
Phenylalanine (Phe, F)
Tryptophan (Trp, W)
AMIDES Asparagine (Asn, N)
Glutamine (Gln, Q)

Amino Acid Structure

Amino acids vary on their structure.
Classification of Proteins Based on Composition
General Classes

1. Simple proteins – with polypeptide chains

SUBCLASSES SOLUBILITY OTHER PROPERTIES EXAMPLES
FUNCTIONS
ALBUMINS Soluble in water Coagulated by heat and Egg albumin, myogen of
Dilute in aqueous solutions usually deficient in glycine muscle, serum albumin of
Precipitate from solution by blood, leucosin of wheat,
saturation with ammonium lactalbumin of milk, and
sulfate legumelin of peas
GLOBULINS Soluble in dilute solutions Coagulated by heat and Ovuglobulin of egg yolk,
but are insoluble generally contain glycine serum globulin of blood,
(euglobulins) or sparingly **Deficient in methionine myosin of muscle, edestin of
soluble (pseudogloblulins) in hemp seed, phaseolin of
water. Precipitate from beans, legumin of peas,
aqueous solution half excelsin of brazil nut, arachin
saturated with ammonium of peanuts, and amandin of
sulfate almonds
GLUTELINS Insoluble in neutral solvent Occur only in plants Glutenin in wheat and
but are soluble in dilute oryzenin of rice
solutions of acids and bases
SCLEROPROTEINS OR Insoluble in most ordinary Entirely animal proteins and Keratin of hair, hoofs, horn,
ALBUMINOIDSS solvents like water, salt are chief constituents of nails, elastin of connective
solutions, dilute acids, alkalis, exoskeletal structures tissue and ligaments,
and alcohols collagen of bones, cartilage
and tendons, fibroin and
sericin of silk
PROLAMINS Soluble in 70%-80% alcohol Generally yield much proline Gliadin of wheat, hordein of
(others in 50%-90%) upon hydrolysis but are barley, kafirin of kafir corn
Insoluble in water, neutral deficient in lysine; plant and zein of corn
solvents or absolute alcohol protein found principally in
seeds

2. Conjugated proteins- simple proteins combined with some non-protein substances

SUBCLASSES OCCURRENCE PROSTHETIC GROUP EXAMPLE
NUCLEOPROTEINS Most abundant in both plant Nucleic acids Nucleohistone,
and animal tissues that have nucleoprotamine
a large proportion of nuclear
materials such as yeast,
asparagus tips, thymus and
sperm
GLYCOPROTEINS Many membrane proteins Carbohydrates Immunoglobulin G
and most proteins secreted
by eukaryotic cells like
antibodies
LIPOPROTEINS Phospolipid protein Lipids B1 Lipoprotein of protein
complexes also called
lecithoproteins are widely
found in plants and animas.
Materials such as milk,
blood, cell nuclei, egg yols,
cell membrane, and
cchlroplasts; also found in
bacterial antigen and viruses
PHOSPOPROTEINS Multi-functional protein that Phosphate groups Milk casein, vitellin of egg
plays multiple roles in viral yolk
transcription
HEMAPROTEINS Proteins linked to a Heme (iron porhyrin) Hemoglobin, cytochromes,
nonprotein, iron-bearing catalase, peroxidase
component
 FLAVOPROTEINS Removal of radicals Flavin Succinate dehydrogenase
contributing to oxidative Nucleotides
stress, photosynthesis, and
DNA repair
METALLOPROTEINS Proteins bound by at least Metal ions Ferritin, plastocyanin
one metal ion *ferritin- storage form of iron
in blood
*transferrin – transport form
of iron in blood

Four Levels of Protein Organization

A. PRIMARY STRUCTURE- refers to definite amino acid sequence in a protein brought about by stable, covalent peptide bonds
B. SECONDARY STRUCTURE- refers to the regular repetitive conformation of AA that are spatially closed to one another; folded
arrangement of polypeptide, stabilized by H bond, disulfide bridge

TYPES OF SECONDARY STRUCTURES

Alpha helix Right-handed helix with 3.6 amino acids per turn, helix
rises 5.4 Angstroms for each turn; stabilized by H bonding
between the carbonyl oxygen of one peptide bond and the
amide hydrogen of another peptide bond 4 amino acid
residues away
Beta pleated sheets Repeating units of amino acids with small compact R
groups can be parallel or anti-parallel

C. TERTIARY STRUCTURE- three-dimensional structure resulting from R-group interactions; coils may be looped, twisted or folded
upon itself in a variety of ways.

Types of R group Interactions

1. H bond
2. Disulfide bond
3. Hydrophobic interaction
4. Electrostatic interaction

Classification based on three-dimensional structure

1. FIBROUS PROTEINS – consist of polypeptide chains arranged side by side in long filaments; tend to be mechanically
strong and insoluble in water
Example: collagen – principal constituent of connective tissue in animals
2. GLOBULAR PROTEINS – coiled into compact , roughly spherical shape; generally soluble in water and are mobile
with cells
Example: hemoglobin, immunoglobulin

D. QUATERNARY STRUCTURE- concerns interactions by which two or more polypeptide

chains associated in a specific manner to form biologically active proteins; formed by
noncovalent association of tertiary structures; evident among globular proteins
 Oligomer – two or more polypeptide (protomers or subunits)

Example: hemoglobin (tetramer), tobacco mosaic virus

Denaturation of Proteins
A protein is defined by its primary, secondary, and tertiary structure. This gives the protein certain identifying properties-
biological, enzymatic, solubility, ionic, reactivity of side group, MW and size – NATIVE STRUCTURE

“Any changes in the native structure results in DENATURATION, brought about by disruption of forces that stabilize the secondary,
tertiary and quaternary structures”
 Determination of the Primary Structure of Proteins
Significance of sequence analysis

1. Protein’s mechanism of action

2. Gene structure
3. Chemical synthesis of medically useful peptides

Determination of Amino Acid Composition

1. Breakdown the polypeptide chain into its constituent amino acids

trp, ser, cys, thr

2. Separate the resulting free amino acids

3. Measure the amount of each amino acid

Common Strategy for Sequence Determination

1. Purification of the polypeptide

2. Cleavage of all disulfide bonds
3. Determination of the N-terminal and C-terminal amino acid residues
4. Break the polypeptide into fragments by internal cleavage at specific amino acid residues. Separate the fragments and
determine the AA composition of each.
5. Determine the AA sequence of each fragment to determine as much of the sequence as possible.
6. Order the fragments by repeating steps 4 and 5, using a cleavage procedure of different specificity to generate “overlap
peptides”. This process will yield the complete amino acid sequence.

Specificity of Cleavage Procedures Used for Sequence Analysis

I. Terminal Cleavages
CHEMICAL METHOS
METHODS REAGENT SPECIFICITY
Sanger’s method 2,4-dinitrofluorobenzene (DNFB) Forms a DNP derivative with N-
terminal AA and epsilon amino group
of lysine
Edman degradation Phenylisothiocyanate (PITC) Forms a PTH derivative with N-
terminal AA
Dansyl chloride treatment Dansyl chloride Forms sulfonamide derivative with N-
terminal AA
Hydraznolysis Hydrazine Hydrolyzes all peptide bonds and
releases free C-terminal AA
ENZYMATIC METHODS
METHOD SEPCIFICITY
Aminopeptidase Cleaves peptide bond involving the carboxyl side of N-terminal AA
Carboxypeptidase Cleaves peptide bond involving the amino side of C-terminal AA

Internal Cleavages
CHEMICAL METHOD
REAGENT SPECIFICITY
Cyanogen bromide Cleaves peptide bond involving the carboxyl side of met residues
ENZYMATIC METHOD
ENZYME SPECIFICITY
Trypsin Cleaves peptide bond involving the carboxyl side of basic amino acids (arg, lys)
Chymotrypsin Cleaves peptide bond involving the carbonyl side of aromatic amino acids (phe, trp, tyr)
and leu
 Thermolysin Cleaves peptide bond involving the amino side of aromatic amino acids (phe, trp, tyr)
and amino side of amino side of (phe, trp, tyr) and amino acids with bulky non-polar side
chains (leu, ile, val)

Enzyme Structure
COFACTORS Enzymes require inorganic ions or complex organic molecules for their activity, non-
protein components are generally called cofactors
ENZYME INORGANIC ION REQUIRED
Peroxidase Fe (Iron)
Cytochrome oxidase Cu (Copper)
Carboxypeptidase A Zn (Zinc)
Nitrate reductase Mo (Molybdenum)

COENZYMES Also called organic cofactors:

1. Flavin adenine dinucleotide (FAD)
2. Nicotinamide adenine dinucleotide (NAD)
3. Tetrahydrofolate (THF)
4. Coenzyme A (CoA)
PROSTHETIC GROUP Present in enzyme and non-enzyme proteins, always tightly attached to the proteinous
part of the enzyme
HOLOENZYME Refers to the apoenzyme along with the cofactor which is complete and catalytically
active
APOENZYME Refers to the inactive form of the enzyme which activates upon the bonding of a
cofactor

Enzyme Classification
International Classification of Enzymes
CLASS SELECTED SUBCLASSES TYPE OF REACTION EXAMPLE
CATALYZED
Catalyze oxidation-reduction reaction involving substrate molecules.
Oxidases Oxidation of a substrate Lactate dehydrogenase
Reductases Reduction of a substrate  Liver – viral hepatitis, cirrhosis
Dehydrogenases Introduction of a double etc.
bond (oxidation) by formal  Heart – acute myocardial
removal of H2 from the infarction (AMI), coronary heart
substrate, the hydrogen disease(CHD), myocarditis
OXIDOREDUCTASES
being accepted by a  Skeletal muscle – muscular
coenzyme dystrophy, muscle trauma
 Kidney
 Erythrocyte (RBC)

*LDH – not clinically significant

Lactate + NAD -> pyruvate + NADH
Catalyze the transfer of functional groups between two substrates
Transaminases Transfer of an amino group Glucokinase
TRANSFERASES between substrates
Kinases Transfer of a phosphate Glucose + ATP -> glucose 6-phosphate +
group between substrates ADP
 AST – Aspartate Aminotransferase
ALT – Alanine Aminotransferase
Catalyze substrate hydrolysis reactions
Lipases Hydrolysis of ester linkages Lipase
in lipids
Proteases Hydrolysis of peptide Triacylglycerol + H2O -> Glycerol + 3 fatty
linkages in proteins acids
Nucleases Hydrolysis of sugar
HYDROLASES
phosphate ester bonds in
nucleic acids
Carbohydrates Hydrolysis of glycosidic
bonds in carbohydrates
Phosphatases Hydrolysis of phosphate
ester bonds
Catalyze the addition of a group to a double bond or the removal of a group
Dehydrases Removal of water from a Pyruvate decarboxylase
substrate
LYASES Decarboxylases Removal of CO2 from a Pyruvate -> acetaldehyde + CO2
substrate
Deaminases Removal of NH3 from a
substrate
Catalyze the conversion of a substrate into another compound that is isomeric with it
Racemases Conversion of D to L isomer Phosphoglucomutase
or vice versa
ISOMERASES Mutases Conversion of one Glucose 1-phosphate -> gliucose 6-
structural isomer to another phosphate
Epimerases Conversion of one sugar
epimer to another
Catalyze the bonding together of 2 substrate molecules with the participation of ATP
Synthetases Formation of a new bond Asparagine synthetase
between substrates, with
LIGASES participation of ATP Aspartate + NH3 + ATP -> Asparagine + AMP
Carboxylases Formation of a new bind + PPi
between substrate and CO2,
with participation of ATP

Enzyme Activity and the Factors that Affect It

Enzyme Activity – measure of the rate at which an enzyme converts substrate to product. It can be determined by
measuring the amount of substrate that has disappeared or the amount of product formed per unit time in the reaction
mixture.
 Coenzymes in Biological Oxidation
1. Nicotinamide adenine dinucleotide (NAD+) and nicotinamide dinucleotide phosphate (NADP+)
2. Flavin adenine dinucleotide (FAD+) and Flavin mononucleotide (FMN)
3. Ubiquinone (Coenzyme Q, CoQ)
4. Cytochromes
5. Coenzyme A
Water and Polarity
o Electronegativity – tendency of an atom to attract electrons to itself in a chemical bond (i.e. to become negative)
o Polar bonds – bonds in which 2 atoms have an unequal sharing in the bonding electrons
o Nonpolar bonds – bonds in which 2 atoms share electrons evenly
o Dipoles - molecules with positive and negative ends due to an uneven distribution of electrons in bonds
o Salt bridge – an interaction that depends on the attraction of unlike charges
o Van de Waals forces – noncovalent associations based on the weak interaction of transient dipoles for one another
o Van der Waals radius - the distance between an atom’s nucleus and its effective electronic surface

Water is a bent molecule with a bond angle of 104.3 degrees, and the uneven sharing of electrons in the two bonds is not
cancelled out as it is in CO2. The result is that the bonding electrons are more likely to be the oxygen end of the molecule
than at the hydrogen end. Bonds with positive and negative ends are called polar.