BIOCHEM MIDTERM  - charge: aspartic acid or aspartate (Asp) and  Our bodies naturally produce enzymes.

glutamic acid or glutamate (Glu)  Anselme Payen named the Enzyme

ENZYMES  Lowers the energy required
PROTEIN: PROTEIN STRUCTURE  activated when a specific substrate binds to
 large and complex molecule  condensation of amino acids forming peptide their active site (specific shape). they are called
 structure, function, and regulation of the body’s bonds. enzyme-substrate complex.
tissues and organs.  Primary Structure: the sequence of amino acids  ENZYMES catalyzes 5, 00 types of Biochemical
Ligand- Gated Channels linked together to form a polypeptide chain reactions
 Open when a neurotransmitter latches onto it’s  Secondary Structure: is determined by the
receptor dihedral angles of the peptide bonds. PHYSICOCHEMICAL NATURE OF ENZYME
Amino Acids  Tertiary Structure: by the folding of protein 1. All enzymes are protein in nature.
 Building blocks of proteins, chains in space. a) Simple protein: made up of amino acid subunits
 Building proteins, hormones, and  joined together by peptide bonds
neurotransmitters. NUCLEOTIDES b) Conjugated protein : prosthetic group
 meat, fish, and soybeans.  basic building block of nucleic acids (RNA and 2. Changes on the pH of the medium
DNA). 3. Heat labile or easily altered by heat
 consists of a sugar molecule attached to a 4. Water soluble
phosphate group and a nitrogen-containing 5. Colloids that are soluble in water posses
base. extremely low rates of diffusion
 adenine 6. Work best at temperatures between 35 to 40
 (A), cytosine (C), guanine (G) and thymine (T). degree Celsius.
7. Dependent on the pH of the medium
DIFFERENT FUNCTIONS OF PROTEINS IN OUR BODY 8. Highly selective
1. Proteins used as antibodies 9. Contain 16% weight as nitrogen
 Non- polar: alanine, valine, leucine, proline, 2. Proteins as a messenger 10. Unique characteristics such as shape
methionine, tryptophan, glycine, isoleucine, and 3. Proteins as structural components 11. Have an active site for target molecules called
phenylalanine 4. Proteins as transport and storage substrates
 Polar: serine (Ser), threonine (Thr), cysteine 5. Proteins as enzymes 12. Larger in size than their substrates.
(Cys), asparagine (Asn), glutamine (Gln), and 13. Not used up or permanently changed by the
tyrosine (Tyr). ENZYMES reaction.
 + charge: Lysine, Arginine, Histidine  help speed up metabolism, or the chemical 14. Can be recycled
reactions in our bodies.
15. Can be regulated by feedback and genetic 1. Oxidoreductases: Catalyzing oxidoreduction B. TRANSFER OF ELECTRONS
mechanisms between two substances OXIDASES – are enzymes which catalyze the removal
2. Transferases: Catalyzing a transfer of group, of hydrogen from a substrate and pass it directly to
other than hydrogen, between a pair of oxygen
substrates.  Dehydrogenases – activate H atoms of organic
3. Hydrolases: Catalyzing hydrolysis of ester, compounds
ether,peptide, glycosyl, acid-anhydride, C-C,  Catalase – acts on hydrogen peroxide to give
C-halide or P-N bonds water and oxygen
4. Lyases: Catalyzing removal of groups from  Peroxidases – act on organic peroxides giving
substrates by mechanisms other than nascent oxygen
hydrolysis, leaving double bonds  Tyrosinase – acts on tyrosine
5. Isomerases: Catalyzing inter conversion of optic,  Ascorbic acid oxidase – acts on ascorbic acid
geometric or positional isomers.
6. Ligases: Catalyzing linkage of 2 compounds C. SPLITTING OR FORMING A C-C BOND
coupled to the breaking of a pyrophosphate DESMOLASES – catalyze the linkage not broken by
bond in ATP or a similar compound water; splitting or forming a C-C bond

CLASSIFICATION OF ENZYMES ACCORDING TO D. TRANSFER OF A RADICAL

CHEMICAL REACTION CATALYZED A. TRANSAMINASES – catalyze the transfer of amino
CO-FACTORS OF ENZYMES groups from amino acids to ketoacids and thus
A. HYDROLASE promote the formation of new amino acids
CO-FACTORS  Carbohydrase – aid in the hydrolysis of
 Assisting enzymatic catalysis carbohydrates( lactase, maltase) ENZYMES WITH THEIR SOURCES AND USES
 Co-enzyme : nonprotein organic compounds  Esterases – aid in the hydrolysis of (Commercial, Pharmaceutical and Medicinal)
(e.g. FAD - Flavine Adenine Dinucleotide NAD – esters( lipases, phosphatse) 1. PROTEOLYTIC ENZYMES
Nicotinamide Adenine Dinucleotide commonly  Nucleases – aid in the hydrolysis of nucleic acids a) Pepsin: Enzymes in digestion
found in vitamins, FMN – Flavine (nucelotidases) b) Alcalase: additive to remove protein stains
Mononucleotide)  Amidases – aid in the hydrolysis of c) Bromelains: mixture of protein-digesting & milk
REACTIONS: amides( ureases) clotting enzymes from the juice of Ananas
1. Co-enzyme + apoenzyme – holoenzyme  Proteases – aid in the hydrolysis of comosus
2. Metal ion activator + apoenzyme – holoenzyme proteins( pepsin, trypsin) d) Papain: breaks down proteins
 Peptidases – hydrolyze peptides to simple e) Trypsin: Converts proteases and peptones to
SIX MAJOR CLASSIFICATION OF ENZYMES peptides and amino polypeptides and amino acids, Secreted by the
acids( aminopolypeptidases,dipeptidases) pancreas
f) Sutilains: Use in Wound Debridement i. Cellulase: Preparation of coffee liquid concentrate CLINICAL ENZYMOLOGY: Enzymes are commonly
g) Rennin: It curdles the soluble casein in milk j. Lactase: Prevention of lactose crystals in ice cream used in medicine
h) Erepsin: Found in the intestinal juice, Converts k. Pectinase: Clarification of wines and juices
proteoses and peptones into amino acids NUCLEIC ACID
i) Streptokinase: Use: treatment of pulmonary ESTERASES  large biomolecules that play essential roles in all
embolism, deep vein thrombosis, arterial a. Lipase: widely distributed in the animal and cells and viruses
thrombosis and embolism, arteriovenous vegetable kingdom, found in the pancreatic juice of  Nucleotides linked by 3′, 5′phosphodiester
cannula acclusion and coronary artery animals and in oily seeds bonds
thrombosis b. Pectase: Splits pectin into pectic acid and methyl  Sequence always specified as 5′→3′
j) Urokinase: Use: treatment of pulmonary alcohol
embolism, coronary artery thrombosis, and c. Steapsin: Lipolytic enzyme capable of digesting BIOLOGICAL SIGNIFICANCE:
restoring the patency of intravenous catheters dietary fat  Responsible for storage and transmission of
OXIDIZING ENZYMES d. Urease: Used as a laboratory reagent for genetic information code
i. Peroxidase: Bring about the oxidation reactions converting urea to ammonia
that cause the discoloration of bruised fruits OTHERS PROPERTIES OF NUCLEIC ACIDS:
ii. Thrombin: Converts the fibrinogen of the a. Collagenase: An enzyme preparation obtained 1. Insoluble in alcohol
circulating blood into the insoluble fibrin of the blood from fermentive cultures of Clostridium histolyticum 2. Slightly soluble in cold water but readily
clot b. L-Asparaginase An enzyme obtained from cultures dissolved in hot water and dilute alkalies
3. Precipitated by HCl and by excess of acetic
of certain stains of Escherichia coli
acid
CARBOHYDRASE/AMYLOLYTIC ENZYMES c. Lipoxygenase: Bread – whitening
a. Amylase: found in the salivary glands, digestive aid
2 TYPES OF NUCLEIC ACIDS:
in pre-cooked foods THEORIES EXPLAINING THE MODE OF ENZYME
1. RNA – Ribonucleic acid: using the genetic
b. Diastase: A yellowish white, amorphous powder ACTION
information encoded in DNA to produce the
obtained from an infusion of malt I. FISCHER’S LOCK AND KEY THEORY
thousands of proteins found in living organisms
c. Amylopsin: sometimes called “animal diastase  The active site of the enzyme and substrate
2. DNA
d. Invertase or sucrase: aids in the hydrolysis of have complementary structures, hence they fit
 Deoxyribonucleic acid the nucleic acid that
sucrose into glucose and fructose together as a key fits a lock
stores genetic information
e. Zymase: Fermenting enzyme causing the II. KOSHLAND'S INDUCED FIT THEORY
 Base pairing rule: A = T
conversion of monosaccharides  the substrate still needs to fit into the enzyme
G=C
f. Emulsin: breaks down glycosides like a key, but instead of simply fitting into
 Double Helix, Anti-parallel – one side runs fr. 5’-
g. Myrosin: Hydrolyzes sinalbin, sinigrin and other the“keyhole,” some type of modification is
3’ while the other side runs Fr. 3’-5’ (opposite)
glycosides induced in the substrate, enzyme, or both. The
DNA TYPES
h. Amyloglucosidase:Production of dextrose from modification begins the process of the reaction.
starch
 A-DNA: right-handed double helix,anti-parallel 2. Ribosomal RNA (rRNA): It is used as a structural  DNA helicase: enzymes that unwinds double
with each other and not symmetrical component of the ribosome. helix
 B-DNA:the canonical right-handed DNA helix 3. Transfer RNA (tRNA): Carry specific amino acids to  DNA primase: primer binds to the 3' end of the
that is the most common form of DNA the ribosomes and decodes the genetic information strand
 Z-DNA: is a left-handed DNA where the double in mRNA in terms of proper amino acid sequence  DNA polymerases: are responsible creating the
helix winds to the left in a zig-zag pattern. new strand by a process called elongation
 DNA ligase: Makes covalent bonds to join
HISTORY OF DNA DNA strands; Okazaki fragments, and new
 Friedrich Miescher( 1869):coined the term segments in excision repair
‘nuclein’
 Richard Altman call substance ‘nucleic acid’ PROTEIN SYNTHESIS
 Phoebus Levine four bases of DNA  creation of proteins by cells that uses DNA, RNA,
 Linus Pauling protein also found in chromosome and various enzymes. It generally includes
was probably the hereditary factor replication, transcription and translation.
 Frederick Griffith inject pneumonia bacteria in
mice PROCESS OF GENE EXPRESSION
 Oswald Avery only nucleic acid caused the PROCESS OF TRANSCRIPTION
change Gene considered the basic unit
 Erwin Chargaff always equal amounts of the of inheritance
bases, pair with one another in some ways  Initiation the phase during which the first
 Wilkins and Franklin x-ray, crystallography, nucleotide in the RNA chain are synthesized
suggest helical structure RNA polymerase bind to a promoter sequence near
 James Watson and Francis Crick discovering the the beginning or gene, reads 3’ to 5’
structure of DNA Promoter relevant protein
TATA BOX able to define the direction of
RNA- Ribonucleic Acid CENTRAL DOGMA transcription and also indicates the DNA strand to be
 Single chain of nucleotides  series of theories of the transmission of read
 Adenine, Uracil, Cytosine, Guanine hereditary information and protein synthesis. Template strand anti-sense strand; Non-template
 genetic information is transferred and strand sense strand
3 FORMS OF RNA: translated into functional proteins,  Elongation: which an RNA complementary to
1. Messenger RNA (mRNA): Serves as cytoplasmic the template strand of DNA
messenger of genes and carrier of genetic DNA REPLICATION  Termination: preventing the inappropriate
information for protein synthesis  Copying a double-stranded DNA transcription of down gene
 Inside the nucleus
PROCESS OF TRANSLATION  DNA Primase: An RNA polymerase that makes 2. Klinefelter Syndrome
Process of forming polypeptide chain from mRNA RNA primers from DNA template  extra X chromosome
codons  RNA Polymerase :Copies RNA from a DNA  Male genetic disorder
 tRNA process at attaching an amino acid to its template  a taller,less muscular body. Broader hips and
respective transfer longer legs and arms Larger breasts (a condition
 Initiation tRNA attaches to the start codon MUTATION called gynecomastia)
 Elongation the polypeptide chains keep  change in a genetic sequence. Down Syndrome/ Trisomy 21
growing, each amino acid has a peptide bond  changes as small as the substitution of a single  have an extra copy of one of these
attaching to it DNA building block, or nucleotide base, with chromosomes, chromosome 21.
 Termination when it reaches a stop codon the another nucleotide base.  the presence of an extra copy of chromosome
translation is finish  MUTAGENS is the substance that causes 21.
Peptide bond long chains of Amino acid mutation either physical or chemical form
 Large scale Mutation : large chromosomal Cri Du Chat Syndrome
INHIBITORS OF PROTEIN SYNTHESIS region  rare genetic disorder that happens because of a
1. Reversible inhibitors in Bacteria ( Bacteriostatic  Point Mutation: a change in one base pair. missing piece (deletion) of a chromosome.
Agents) stops bacteria from reproducing
a. Tetracycline DIFFERENT TYPES OF MUTATION CARBOHYDRATES
b. Chloramphenicol  SILENT MUTATION: “new codon specifies same  “hydrates of carbon” or sugar molecule
c. Erythromycin amino acid”  CnH2nOn or Cn(H2O)n general formula
d. Clindamycin  MISSENSE MUTATION: “New codon specifies
2. Irreversible inhibitors in Bacteria( Bactericidal different amino acid”. the mutation has altered Saccharides: building blocks / fundamental sub-units
Agents) kills bacteria. the protein of carbohydrates
a. Streptomycin  NONSENSE MUTATION: “new codon is stop
IMPORTANT ENZYMES IN CENTRAL DOGMA codon”. if the stop codon is generated the Storage forms of Carbohydrate:
resulting protein will be partially complete. Glycogen: storage form of carbohydrate in animal
 DNA Gyrase: Relaxes supercoiling ahead of the  FRAMESHIFT MUTATION: addition or loss of tissue which is found in liver and muscle.
replication fork DNA DNA bases changes a gene’s reading frame. Starch: storage form of carbohydrate in plant tissue
 Ligase: Makes covalent bonds to join DNA
strands; Okazaki fragments, and new segments FOUR CHROMOSOMAL ABNORMALITIES Biological Significance:
in excision repair 1. Turner Syndrome 1.) The main source of energy in the form of ATP
 DNA Polymerases: Synthesize DNA; proofread  female-only genetic disorder 2.) Other carbohydrate metabolic products are used
and facilitate repair of DNA  medical and developmental problems, including in the synthesis of other types of compounds.
 Helicase Unwinds double-stranded short height, failure of the ovaries to develop Metabolism: process of breaking down into simplest
and heart defects. forms
e.g synthesis of fatty acids and amino acids a. Lactose: milk sugar least soluble and least sweet of I- CELLULOSE GROUP:
3.) Help in the breakdown of food stuff by acting as all sugars Cellulose:
catalyst or promoters of oxidation. b. Maltose: malt sugar found in germinating grains  most abundant organic compound making up
and in malt; are among the series of substances about 50% or more of the carbon vegetation
CLASSIFICATION OF CARBOHYDRATES formed by the hydrolysis of starch  Purest source is cotton
I. SIMPLE SUGARS/MONOSACCHARIDES c. Cellobiose: obtained from the hydrolysis of
 these are CHO’s that cannot be hydrolyzed to cellulose from wood & cotton  Pentosans – ( C5H8O4)n – x H2O – long chain of
simplest forms. pentose units
 General formula CnH2nOn Non- reducing sugars: are those whose aldehyde 1. Xylans – found in wood, straw, rice bran and corn
 Functional group present Aldose ( Aldehyde groups are involved in the linkage,no free aldehyde cobs
group) Ketose (Ketone group) or ketone group 2. Arabans – found in gum Arabic, mucilage and fruit
a. Disaccharide/s juices.
Based on the no. of C-atoms in the molecule Sucrose Hexosans – ( C6H10O3)n – x H2O
a. Triose: (C3H6O3) – not found free in nature but as  a.k.a table sugar, cane sugar, saccharose, beet 1. Glucosan – starch yielding glucose
products of carbohydrates metabolism. sugar 2. Agar agar
b. Tetroses – 4-C monosaccharide, (C4H8O4)  most widely distributed in nature
c. Pentoses – 5-C monosaccharide, Ribose:  obtained commercially from sugar cane and Dextran
constituent of RNA sugar beets  Polysaccharide produced by certain
d. Hexoses – 6-C monosaccharide  α-D glucose + β-D fructose microorganisms when grown on sugar media
- are the most important monosaccharides found in  connected by alpha 1-2 glycosidic linkage.  Used as blood extender due to its high viscosity,
plants. * Honey contains invert sugar. Invert sugar is sweeter osmotic pressure, low disintegration and
e. Heptoses – 7- C sugar form a vital importance in than sucrose. utilization
the glucose metabolism of animals and in the b. Trisaccharide/s – C18H32O16 Hexopentosans
photosynthesis process of plants Raffinose Pectins:
f. Octose – 8 – carbon sugar isolated from avocado  forms in sugar beets  Colloidal carbohydrates
pulp  made up of glucose, fructose and galactose.  Responsible for jellying properties of fruits
c. Tetrasaccharide/s – yield for monosaccharide  On hydrolysis it yields arabinose, galactose,
B. OLIGOSACCHARIDES – carbohydrates which on molecules on hydrolysis acetic acid, methyl alcohol and galacturonic acid
hydrolysis will yield 2-10 units  Stachyose – fructose + glucose + 2 molecules of
● Disaccharides (C12H22O11): considered as the galactose HETEROPOLYSACCHARIDES:
most abundant oligosaccharide C. ) POLYSACCHARIDES ● Polysaccharides which on hydrolysis yield mixtures
1. ) Reducing disaccharides – those which contain a  more than 10 saccharides of heteropolysaccharides and derived products
free aldehyde or ketone group  more complex, high ocular weight ● 2 MAIN GROUPS:
a. Neutral mucopolysaccharides: Made up of N-  Only GAG with no uronic acid A. Hydrolysis
acetyl-hexosamine and hexose  Found in cornea and tendon Agents of Hydrolysis:
Example: those occurring in bacteria and so-called 2 types  1. Heat
“mucoids” including important immunological, ▪ Keratan sulfate I – found in cornea  2. Acid
specific blood group substances ▪ Keratan sulfate II – found in skeletal muscle  3. Bases
b. Acid mucopolysaccharides: Contain hexuronic acid,  4. Enzymes
sulfate or phosphate Dermatan sulfate B. Starch Hydrolysis
 Found in Skin , Blood vessels ,Heart valves & C. Fermentation
HYALURONIC ACID Cornea  Complex process which involves the breaking
 Serves as a cementing substance in the tissues  Its’ presence in the Sclera maintains overall down of complex substances with the aid of
which allows the passage only of the shape of the eye . biological catalysts called Enzymes
metabolites but not the infecting  Major GAG synthesized by arterial smooth  Ethyl alcohol + CO2 are the products of
microorganisms. However it is fragmented by muscle cells fermentation
hyaluronidase (“spreading factor”) from D. Osazone Formation
bacteria,allowing the diffusion and spread of Heparin  Reagent: Phenylhydrazine
bacterial infection  Contains D-glucoronic acid + glucosamine  (+) Result: yellow crystals or yellow ppt.
 it is the only intracellular GAG
HEPARINE (heparin): An important acid  It is an anticoagulant E. Molisch Test
mucopolysaccharide secreted by the lung tissues and  a general test for carbohydrates except trioses
certain types of cells lining the arterial I- PHYSICAL and tetroses which lack the minimum requisite
blood vessels A. Monosaccharides and Oligosaccharides: of 5C atoms
1. White crystalline solids  Reagent: α – naphthol + conc. H2SO4
Five Glycosaminoglycan(GAG )/Mucopolysaccharides 2. Soluble in water  (+) Result: violet ring at the junction
Hyaluronic acid: 3. Optically active – due to the presence of a chiral  F. Oxidation: Aldehyde - Acid
 Contains D-glucoronic acid + glucosamine carbon  G. Reduction: Aldehyde – Alcohol
 Present in high concentration in testes, seminal Polysaccharides are:
fluid, & in certain snake and insect venoms. 1. Amorphous solid
 Serves as a lubricant and shock absorbent in 2. Low molecular weight form a colloidal dispersion
joints in H2O
Chondroitin sulfate 3. High molecular weight are insoluble in H2O (eg.
 Most abundant GAG in the body. Cellulose)
 It is present in cartilages, tendons, ligaments, 4. Not sweet / no flavor at all
and aorta which helps to maintain their shapes.
Keratan sulfate II- CHEMICAL