BIOCHEMISTRY LAB NOTES Maam Minerva Daya & Maam Gladys Ilagan

Formulas

ACID-BASE RXN, pH Acid + H proton donor e- acceptor Base OH proton acceptor e- donor

Arrhenius Bronsted- Lowry Lewis

H2O - Amphoteric - As base when paired with stronger acid - As acid when paired with weaker base

Strong acid/ strong base Forward rxn ( complete ionization/ disassociation) Ka>1, Kb>1 Weak acid Backward rxn ( incomplete ionization) Less product Ka<1, Kb<1

acidic basic neutral

pH>7 pH<7 pH=7

If HA is a strong acid [HA] is the same with [H3O+] Ex. 0.10M HCl [H3O+] = 0.10M pH = -log[H+] = - log[0.10M]= 1

Mole Fraction

1-x Mole Percent % I C E

0.10 -x 0.10 - x
-5

0 +x x

0 +x x

Ka = 1.8 x 10

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= 1.34 x 10

-3

If x <<< HA, then

Ex. What is the amt in grams of TRIS base and volume of 6M HCl needed to prepare 0.50M TRIS-HCl -6 Kb TRIS-HCl = 1.19 x 10 , 2.0L, pH=8.5 HA (Ka = 8.40 x 10 )
-9

pH = -log(

Titration of Polyprotic Depends on the pH you need Henderson-Hasselbach pH

--- max buffering capacity *salts of WB produce acidic soln

pH Measurement and Buffer preparation Buffer weak A and conj B HA and A (salt) + - weak B and conj A B and BH (salt) Properties - pH is independent of dilution not so much change in pH - add acid neutralize by A - add base neutralize by HA Buffering Capacity - ability of buffer to resist change in pH - no. of moles of strong acid/base that causes 1.00L of the buffer to undergo a 1.00 unit change in pH - *its always positive Affected by: - Concentration Ratio of component s( - Total concentration of components Maximum Buffering Capacity pka is near pH = 1.82 Gen. Criteria of Biological Buffers 1. pka between 6 and 8 2. water soluble 3. exclusion by biological membranes
-

Hendersen-Hasselbach Equation

BUFFER - Soln of o Weak base + Conj. acid o Weak acid + Conj. Ase - Resists sudden change in pH Ex. What are the amounts of acetic acid and sodium acetate needed to prepare 1.5M acetate buffer, 500 mL, pH 5.00?

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4. minimal salt effects 5. minimal effects on the dissociation from changes in temp and conc 6. minimal interaction between buffer components and critical rxn components ( would act as expectator ion; noninteractive) 7. chemical stability 8. light absorption 9. ease of use Buffer Preparation - prepare at RT, adjust pH at temp at w/c it will be used - test pH - adjust pH with SA or SB

From pH5 to pH 4 I C E 0.035 x 250 = 8.75 + 12.50 21.25 0.0850 x 250 - 12.50 3.75

- 12.50

From pH 5 to pH 6 8.75 7.45 1.30 mmol

16.25mmol 7.5 23.75mmol

pH - acidity/ basicity + - - log[H ] PROTEINS Difference between Actual and Theoretical pH value + - Activity of H - pH of water pH meter - pH electrode - reference electrode - high input meter pH 4, 7, 10 std pH pH calibration - accurate pH reading - std are working properly - check if pH meter is working properly alternating double-single bonds Conjugation -highly absorption of light pH indicator vs pH meter pH : low conc of H ex.
+

ISOLATION AND CHARACTERIZATION OF PROTEINS Levels of protein structure Primary aa sequence Secondary aa near each other Tertiary- aa far from one another; 1 polypeptide Quaternary- several polypeptide chains Classification of proteins - Acc. To composition 1. Simple 2. Conjugated simple proteins + non-proteins - Acc. To biological function 1. Catalyst 2. Transport protein 3. Nutrients and storage 4. Structure 5. Contractile and motile 6. Defense 7. Regulatory - Acc. To shape 1. Globular 2. Fibrous - Acc. To solubility 1. Albumin H2O, dil aq soln 2. Globulins dilute salt soln 3. Glutenins dilute acids and bases 4. Prolamin ethanol 5. Albuminoid usual solvents Protein Denaturation Tertiary Structure destroyed lost of protein function Irreversible cant be regained Reversible can be regained Denaturing Agents 1. Strong Acid & bases Hydrolyses amine bonds 2. Organic Solvents 3. Detergents 4. Reducing Agents disulfide bonds reduced SH 5. Salts NaCl, Ammonium Sulfate, KCl - Salting in salts enhances protein solubility - Salting out salts are preferred by H2O; proteins aggregate then precipitates 6. Heavy Metals 7. Temperature Hydrolysis 1. Complete Hydrolysis amino acid products o Strong acid & strong base - ACID disadvantage o CYS and TYR partially destroyed o TRP (complete destruction) black color hydrolysate

To determine conc

1. 250 mL 0.10 M acetate buffer, ph 5.00 =? pH 4 and pH6

[HA] = 0.035M ; [A ] = 0.065M 2. At pH 4.00

-

[HA] = 0.015M ; [A ] = 0.085M 3. At pH 6.00

-3 -

[HA] = 5.21 x 10 M ; [A ] = 0.095M

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o VAL and ILE liberation o Racemization and destruction of o ASN + GLN ASP + GLU *perform hydrolysis aa components - BASE - advantage - TRP- not destroyed - disadvantage - ARG, ASN, GLN, SER - destroyed 2. Incomplete Hydrolysis o Protease- enzymes o Products; aa and oligopeptides - Protease specific in cleaving - Trypsin, chymotrypsin, pepsin, bromelain (pineapple), papain(papaya) *TRYPSIN- c-terminal side of LYS and ARG CHYMOTRYPSIN L-isomers of TYR, PHE, TRP PEPSIN c-terminal to PHE and LEU and to a lesser GLU linkages BROMELAIN carbonyl end of LYS, ALA, TYR, GLY PAPAIN peptide bonds of LEU and GLY

- hydrophobic aggregates then precipitates - net positive: soluble to water ALBUMIN -alpha-lactalbumin -metalloprotein -regulatory protein-lactose biosynthesis -isolated by heat denaturation ( in acidic condition) MYOGLOBIN -isolated by salt precipitation -stores oxygen -hemoprottein containing heme group at its center -helix -1 polypeptide chain GLUTEIN -storage protein -elasticity and extensibility of dough - gliadin and glutein components - isolated by difference in solubility in water - starch- removed by running H20 (+) blue starch (-) Yellow

Separation/ Purification of protein -properties of proteins being considered 1. Charge 2. Molecular size, shape 3. Solubility 4. Affinity to ligand 5. pI pH < pI positive pH > pI negative

Qualitative Color Reactions 1. Biuret Test Peptide bond ( at least 3 aa) CuSO4, NaOH 2+ Formation of coordination of complex of Cu and 4 N atom Purple color solution 2. 3. 4. Ninhydrin (Triketohydinedene hydrate) Alpha amino grp Oxidative decarboxylation and deamination Condensation Blue-violet color Xanthoproteic Test Aromatic aa HNO3, NaOH Nitration of aromatic Millons Test Tyrosine Red color Complexation with Mercury

ISOLATION OF CASEIN & ALBUMIN from Cows Milk

Cow's Milk

Milk Protein

CASEIN

WHEY PROTEIN

Alpha1

Alphalactalbumin

5. Hopkins- Cole Tryphtophan Purple interface *Negative in Millon and Hopkins-Cole -PHENYLALANINE 6. 7. Sakaguchi Arginine Complexation of guanino group Nitroprusside Cysteine or methionine Complexation of nitroprusside

Alpha2

betalactalbumin

Beta

serum albumin

8. Fohls Test Lead Ac PbS (black ppt) *Nitroprusside and Fohls for S-containing aa Kappa 9. Test for Amide Peptide Aspargine and glutamine Evolution of gas ammonia Litmus paper- red to blue

CASEIN -phosphoprotein (phosphate attached to OH) - micelles - Isolated by isoelectric precipitation pH 4.6 - if proteins are net neutral charge
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10. Pauly Histidine, tyrosine

Azodyes (red/orange)

cytosineyellow colorlesspurple 3. Purine 4. Pyrimidine ACID + W-T+Y+ + /+ C+/M+ H+ Y +/ BASE + + + + + + ENZY + +/+ + + + + + +

Tests Biuret Ninhydrin Xanthoproteic

INTACT + + /+

Millon Hopkins-Cole Sakaguchi Nitroprusside Fohls T. for Amides Pauly

+ + + + + + +

ISOLATION OF RNA FROM YEAST -25mL H2O ; 5mL 1% NaOH ; 3g active dry yeast -heat in 15 mins with stirring -strain through cheesecloth -add acetic acid until blue liquid turns to red -HAc to ppt-out the protein - filter to get the protein -beaker: add 20 mL of 95% ethanol, 0.2 mL conc HCl -to ppt protein -decant -UV measurement A260/ A280 Characterization test for RNA 1. Ribose: Bials Orsinol 2. Phosphate: Ammonium Molybdate 3. Purines: Murexide 4. Pyrimidines: Wheeler-Johnson 5. Test for Phosphate - Usually negative - Phosphate buffer/ coke as std - Sulphuric acid slide sa slide very slowly - Boiling H20 bath - Cool before adding conc. HNO3 (proceed even without white fumes) Ammonium Molybdate (+) result yellow ppt ENZYMES

Paper Chromatography -aa composition -visualized using ninhydrin -

DNA -double helix Purine pyrimidine hydrogen bond A=T GC Doexyribose - ribose is a sugar (cyclic) Alternating S and P --phosphodiester bond Onions - easily available * nuclear ratio compared to cytoplasmic ratio percentage yield in isolation Cytoplasm site of protein synthesis (relative to nucleus) -bec of organelles Nucleus ISOLATION OF DNA from ONIONS -50mL of homogenizing soln Medium onions -warm for 5min (@ 60 degress) -papain (meat tenderizer) -warm for 10 min -transfer immediately -ice bath to stop destruction of DNA -incubate for 5 min while swirling -transfer into a blender -homogenizing for 1 min -Cheesecloth ( filter) -add 20mL ice-cold ethanol -let stand for 5 min -DNA: slimy white red -using Pasteur pipette -transfer the DNA into a clean test tube -PE buffer or SSC solution (5mL) -UV measurement -260nm nucleic acid -280nm protein - should be higher -acid hydrolyse break H-bond, glycoxylic bond, phosphodiester Characterization test for DNA 1. Deoxyribose (Dische) std: brown soln with black ppt 2. Phosphate *guanine yelloworangepurplecolorless

Ways of determining the activity of an enzyme 1. The amount (conc) of the substrate remaining 2. The amount (conc) of the product formed Factors affecting enzyme activity 1. pH 2. temp 3. conc. of substrate, when [E] is constant conc. of enzyme, when [S] is constant Sucrose -D-glucose (+)d -D-fructose (-)l linked by 1,4-glycosidic bond Invertase / Sucrase -fructofuranosidase catalyses the hydrolysis of the terminal non-reducing fructofuranoside *anomeric C if free, sugar has reducing property - if nakabind

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CARBOHYDRATE - Polyhydroxyaldehyde - Polyhydroxyketone - Polyhydroxyhemiacetal - -polyhydroxyhemiketal Reaction of aldehyde/ketone with alcohol

Classification of Carbohydrate Acc to the # of the Saccharide units 1. Monosaccharide 3C triose *aldotriose/ketotriose 4C tetrose 5C pentose 6C hexose 2. Disaccharide Maltose Lactose Sucrose 3. Oligosaccharide 10-15 saccharide units 4. Polysaccharide Starch Glycogen

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