The document is a comprehensive overview of fundamental biochemistry concepts, covering topics such as enzyme action, carbohydrate metabolism, lipid structure and function, protein organization, and nucleic acids. It emphasizes the importance of biochemistry in understanding metabolic processes, clinical diagnosis, and therapy, as well as its application in various biological and medical sciences. Additionally, it discusses transport mechanisms in cells, the properties of water, and the significance of buffers in maintaining pH balance.

1. Biochem-301, 3(2-1) new
Elementary Biochemistry
By
Dr. Zahid Mushtaq

2. Theory
A general introduction to the science of biochemistry. Ionization of water,
weak acid and weak bases, pH, buffers, diffusion, osmosis and
osmotic pressure. Enzymes: Classification, nomenclature,
characteristics, coenzymes, cofactors and prosthetic groups.
Mechanism of enzyme action. Enzyme inhibition. Carbohydrates:
Classification, characteristics, aerobic and anaerobic oxidation of
glucose, biological functions of carbohydrates. Lipids: Composition
and classification, structures of saturated and unsaturated fatty acids
and their properties, characteristics of fats and oils, general
metabolism of fats and oils. Proteins: Composition and classification,
characteristics and classification of amino acids, peptides and levels of
structural organization of proteins, physiological function and general
metabolism of proteins. Nucleic acids: Chemical composition,
structures of DNA and RNA. Functions of DNA and different types of
RNA in the cell.

3. Introduction to Biochemistry
Chemical Structures, reactions, principles and mechanism behind
such interactions with all aspects around Chemistry
Biomolecule’s-Chemical Structures, reactions (Metabolism),
principles and mechanism behind such interactions with life in all its
deverse forms and aspects either directly or indirectly
BioChemistry
Molecular Level
“Molecular logic of Life in all its diverse forms can be explained by
Biochemistry”

4. •Deals with metabolic processes in living tissues a material
called Protoplasm (basis of all life)
•These reactions in Normal way  HEALTHY But
Disorganization SICKNESS/ DEATH
•All components that make life are themselves inanimate but
combinations makes life possible.
•Young emerging science in the 20th
century but now a major
Discipline  dependent on the discoveries of braches of
Chemistry (organic, inorganic, physical , analytical etc), Physiology

5. Scope and importance of Biochemistry
Now it answers to explanations for the mechanisms behind Medical
sciences  Physiological, Pharmacology, Bacteriology, Pathology, nutrition,
food sciences etc
Solutions to clinical problems, remedies to deficiencies like Rickets ,
pellegra (B3), Beri-Beri (B1 Thiamin), Scruvy, Anemia Diagnosis and therapy
Purifying vitamins, hormones (insulin), Anti-toxins, vaccines, proteins etc
Enzyme inhibitors (Drugs e.g competitive), Recombinant DNA technology/
genetic engineering , cloning , DNA profiling (identification)
Mysteries in agriculture, industry, research and all life sciences

6. Books recommended
Principles of biochemistry by Lehninger (4th
edition and onward)
http://www.irb.hr/users/precali/Znanost.o.Moru/Biokemija/Literatura/Lehninger%20Principles
%20of%20Biochemistry,%20Fourth%20Edition%20-%20David%20L.%20Nelson,%20Michael%20M.
%20Cox.pdf
Medical biochemistry by Mushtaq Ahmed vol-1 edition after 2008
Cell and molecular biology by Gerald Karp 3rd
edition and onward
any
http://www.btsdl.cc/cell-and-molecular-biology-by-gerald-karp-6th-edition-tf2432083.html

7. THE CELL
CELL THEORY;
1. All living organisms are made up of cells and cellular components. May be
uni/multi cellulars.
2. Basic structural and functional unit of Life
3. All cells are produced from preexisting cells.
Properties ;
•A high degree of chemical complexity and microscopic organization.
•Systems for extracting, transforming, and using energy from the environment to do work
•Defined functions for each of an organism‘s components and regulated interactions
•Mechanisms for sensing and responding to alterations in their surroundings.
•A capacity for precise self-replication and self-assembly.
•A capacity to change over time by gradual evolution.

9. Plasma membranes and cytoplasm
“The outer periphery of the cell that separates its internal contents from the surroundings.”
1. Lipid and protein molecules
2. Thin, tough, pliable, hydrophobic barrier
3. Selectively permeable by Transport proteins
4. Signals by receptor proteins
5. Membrane enzymes participate in reactions
6. Flexible in shape and functions  less strong bondings
7. Can grow as cells multiply
Cytoplasm:
“The internal volume enclosed by the plasma membrane”
8. Aqueous portion cytosol and particular portions gel
9. Rich in enzymes, RNA, metabolites, macromolecules, coenzymes , Ribosomes and
Proteasomes

10. Movement of materials across membranes
• Cells surrounded by plasma membrane  all
communications through it
• Dual function of membrane 1) must retain the
contents avoid leakage 2) exchange of necessary
materials
• Lipid bilayer is best to protect loss of ions, polar,
amino acids, sugars, hormones etc
• Movements are passively (gradients, no energy )
and actively (energy needed)maintains net flux (one
may exceed other)

11. Passive transport: Simple diffusion, diffusion through
aqueous protein-linked channel, facilitated diffusion
• Spontaneous process in which substances move from
a region of higher concentration to low concentration
till equilibrium
• Exergonic  energy from external source for random
thermal motion / collisions
• If substance Electrolyte movement by chemical
gradient or by Electric Potential gradient i.e. by
concentrations or by difference between charges
electrochemical gradients
• E.g. K+
ions across membrane
++++++++++++++++++++++ 3Na
- - - - - - - - - - - - - - - - - - 2K/Cl-

12. Channels  Move ions nerve impulses,
secretions, muscles contractions, cell volume, open stomata etc
• Integral membrane proteins Downhill
• Always bidirectional till net flux
• Sequence similarities shows this protein
has common ancestry
• Keeps open/close conformations
1. Voltage gated channels: Conformational changes depends on
difference of ionic charges on 2 sides. E.g. K+ channels
2. Ligand-gated: Conformational changes depends on binding of a
specific (ligand) molecule which is not solute itself. E.g.
acetylcholine binds to outer surface to cation channels, cAMP
binds inner to Ca++ channel.
C. Elegans (1000 cells), 90 different genesK+ channels

13. Non-electrolyte diffuses passively…
• Substance must be in high conc at one of
membrane
• Membrane Permeable to it Solute must cross
aqueous pore without
contact with lipid
Solute must cross lipid
layer by dissolving
It must have polarity match
(NON-POLAR)
Partition coefficient: Ratio of solubility
of solute in non-polar solvent
(octanol/veg.oil) to that in water, when
both solvents are mixed together
2 molecules same P.C, then small uncharged will
penetrate faster. E.g. more CO2,O2,H2O, NO etc
& Less sugars, amino acids, P-compounds
require mechanisms
P.C
Pentration
cm/sec
sugars
caffein
Small values less Greater lipid solubility

14. Diffusion of water through membrane best
movement example
• Water usually moves rapidly as compared to
other ions / polar solutes selectively
permeable  membrane  called OSMOSIS
“Water moves readily across a semi-
permeable from a region of lower solute
concentration to a region of higher solute
concentration”
Demonstrated by
placing a cell in a non-
permeable solute
solution of different
concentrations across
plasma membranes
Hypertoni
c
/hyperos
motic
solution
Cells shrink
and own H2O
comes out 
cured by gain
of ions
Hypotonic
/hyposmo
tic soltn
Cells swell by
gaining H2O
from outside
 cured by
loss of ions
Isotonic0.85
% NaCl saline
No net flux
Temporary but best example of movement and
shape changes

15. `

16. Uses
• Digestive tract secrete  Liters of of fluid but reabsorbed by osmosis
 Animals remain in iso-osmotic , but in diahhrea occurs if fails to
reabsorb
• Plant cells hypertonic internally  let H2O inside Turgid (turgor
pressure pushes against cell walls) in hypertonic solutions
plasmolysis
• Aqua porins in some cells more permeable to water kidney/plant
root protein-channels allows this
In congenital nephrogenic diabetes insipidus mutations in aquaporins
vassopressins fail no reabsorbtion higher urine excretions

17. Facilitative diffusions: (fast diffusions by selectively
binding membrane spanning proteins that helps in diffusion)
Solute binds selectively at one end induces
Conformational changes exposing it to other end.
This transporter binds at a side with solute at one
time then to the other side
Similar to enzyme-catalysed reactions;
Specific to even D/L isomers
Obey saturation kinetics i.e. blocked at
saturation
Regulated
Conformational changes are induced (induce fit
model)
Slow rate 100s to 1000s /sec
For Example: GLUT1-5 isoforms, insulin
responsive cells in muscles and adipocytes.
High glucose insulin GLUT4 more
translocated uptake into cells

19. Properties and functions of water
Polar Molecule of H2O
70% by weight Liquid state due to H-bonds
Between
others
Betwee
n each
other
Like dissolves
like , so polar
solutes and
solvents
dissolves by
interrupting
H20-H2O
interactions
Higher melting,
boiling points and
heat of vaporization,
great internal
cohesion are all due
to H-bonds .
Hydrophilics those that dissolve
easily
Hydrophobics & Amphipathics

20. AS SOLVENT

21. Ionization of water, weak acids and bases
Proton hoping
Water is weakly ionizable i.e. few molecules
dissociate although its neutral . Many
properties can also be explained by this.
No free proton exists in
water but forms hydronium
Ionization  Electrical Conductivity and
proton hoping makes it fast (cathode/anode
movements)

22. To express ionization quantitatively
For a reversible reaction we know;
Equilibrium constant Keq = fixed and
characteristic for any given chemical
reaction at a specified temperature.
It defines the composition of the final
equilibrium mixture
For water;
At 25o
C [H2O]=55.5M, for 1L water its
1000/18=55.5
Ionic product
of water
E.C=1 x 10-16
M = Keq

23. At neutral pH we have same
concentrations of both H+ & OH-
Thus when H+ is high OH- should be
Low. Vice versa
Similarly we also know that;
[H+] [OH-] = 1 x 10-14
M2
Taking –log on Both sides ;
–log[H+] –log [OH-] = –log [1 x 10-14
M2
]
Since we know –log [H+]= pH
Thus
pH + pOH = 14
At neutral pH, [H+
]= 1 x 10-7
M

24. pH, pOH, pKa
• pH= - log [H+] where [] represents molar concentration
• Strength of H+ in a solution that indicates the measure of
acidic/basic character. Since addition of acids and bases
changes ions concentration in indexes or powers of 10 and
in decimals. Logarithm changes it into an expressible
whole number forms. i.e. 1 x 10-7
=[H+]= pH=7.0=neutrality
• pOH= -log [OH-]
• pKa = - log Ka (defined as that value of pH at which the
amount of weak acid and its conjugate base are equal) Its
helpful in determining the strength of a buffer as
pKa±1=buffer capacity, Ka is the dissociation constant of
an acid. More values stronger acids highly ionizable.

25. • The pH of an aqueous solution can be
approximately measured with various
indicator dyes, including
litmus, phenolphthalein, and phenol
red, which undergo
color changes as a proton dissociates
from the dye molecule. Accurate
determinations of pH in the chemical or
glass electrode method.
• pH is important in clinical sciences 
acidosis/alkalosis.

26. Buffers
“Are solutions or systems that tends to maintain their own pH
when a small amount of acid or base is added to them”
Chemically two types;
 Acidic = weak acids + conjugate base/salt
For Example, CH3COOH/CH3COO- or CH3COONa acetate
buffer or sodium acetate buffer
• Basic= weak base or its salts
E.G., NH4OH / NH4Cl
Hemoglobin is also a buffering system.

27. • Buffers serve as first line of defense against any foreign
invader, enzyme reactions, cell biology, storage, switch on
off by maintaining structure-function relationships,
microbiology etc.
• Buffer strength is determined by the Molar concentrations
of the components making it (0.5 M + 0.5 M= 1.0 M)
• pKa= 4.76 , pH=4.8 (max capacity around) of acetate buffer.
• Among both components weak acids play a significant role
in determining capacity and properties of a Buffer.
• pKa ±1 = Buffer Capacity
Buffers…….

28. `
• E.g #2: Sodium Phosphate buffers H3PO4/NaH2PO4/
Na2HPO4/ Na3PO4
• CH3COOH + NaOH  CH3COONa + H2O
• CH3COONa + HCl  CH3COOH + NaCl
• Common ion effect suppressed the dissociation of
acid base which change pH, neutral salt / water,
weak acids as products causing little changes in pH.
• Titration with 0.1M CH3COOH 10mL with 0.1M
NaOH to understand buffering action of weak acid
Buffers……. Machanism

30. Preparation of Buffers
• Prepare a PO4 buffer of pH=7.0 of 250 mL
volume with 0.1 M concentration?
Information is required about Potassium and
Sodium phosphate salts or acid that has pKa
values closest to the required pH.
Information of molar ratios of weak acid and
conjugate is required , from Handerson-
hasselbalch equation.
Molar masses required

31. Selection ;
• H3PO4=pKa=2.1
• NaH2PO4=pKa=6.8
• Na2HPO4=pKa=12.2
pH = pKa + log [A-]/[HA]
7.0 = 6.8 + log [A-]/[HA]
0.2 = log [A-]/[HA]
0.2/1 = log [A-]/[HA]
Taking anti-log on both sides to eliminate
log
Anti-log (0.2) = [A-]/[HA]
1.585 / 1 = [A-]/[HA]
Thus molar ratio of salt (Na2HPO4) is
1.585 and acid is (NaH2PO4) = 1
Total ratios = 1.585 + 1 = 2.585
Volumes required;
Vol of Na2HPO4 = 1.585 / 2.585 x 250 mL
= 153.3 mL
Vol of NaH2PO4 = 1 / 2.585 x 250 mL
= 96.7 mL
Check ; 153.3 mL + 96.7 mL = 250 mL

32. To get information of mass or weigh of the salt and acids for making buffer;
We need molar mass of
Na2HPO4 . 2 H2O = 178 g
NaH2PO4 . 2 H2O = 156 g
Amount of Na2HPO4 . 2 H2O = 178 g x 153 mL x 0.1 M
1000
= 2.72 g in total 250ml of salt in buffer solution (dH2O)
Amount of NaH2PO4 . 2 H2O = 156 g x 96.7 mL x 0.1 M
1000
= 1.508 g in total 250ml of acid in buffer solution (dH2O)
Thus first take 200 mL of dH2O and dissolve Na2HPO4 . 2 H2O = 2.72 g and
NaH2PO4 . 2 H2O = 1.508 g and make volume upto 250 mL
Check pH
Check % error
Amount (g)= Mol wt x Molarity x Vol
1000

33. Problem # 2.
Prepare a buffer solution of Na-Acetate
of pH=5.76 , 0.1M of 1 litre volume.
(pKa=4.76 of CH3COOH)

34. Solution
pH = pKa + log [A-]/[HA]
5.76 = 4.76 + log [A-]/[HA]
1 = log [A-]/[HA]
Taking anti-log on both sides to eliminate
log
10/1 = [A-]/[HA]
Total molar ratios = 10 + 1 = 11
Volume of acid = 1/11 x 1000 mL
= 90.9 mL
Volume of salt = 10/11 x 1000 mL
= 909.1 mL
Selection= CH3COOH/ CH3COONa
CH3COOH specific gravity 1.052 g/mL,
99%
Amount of CH3COOH = 60 g x 90.9 x 0.1 M
1000
= 5.45 g in total 1000ml of salt in buffer
solution (dH2O)
Amount of CH3COONa= 82 g x 909.1 x 0.1 M
1000
= 7.5 g in total 1000 ml of acid in buffer
solution (dH2O)
NOTE= FOR SOLID SALT CH3COONa WE CAN
WEIGH BY WEIGHING BALANCE BUT FOR
LIQUIDS LIKE CH3COOH WE NEED TO USE
VOLUMES EQUIVALENT TO MASS
CALCULATED
(Info about purity and sp.gravity will help
here)

35. We know CH3COOH specific gravity= 1.052 g/mL, 99%
that is
1.052 g = 1 mL
1 g = 1/1.052
5.45g = 1/1.052 x 5.45
= 5.18 mL
so 99% pure acid required in vol= 5.18 mL
1% = 5.18/99
100% = 5.18/99 x 100
= 5.3 mL of 99% pure is
required to make a buffer
check pH , calculate % Error, check individually while adding
components which component plays a vital role in pH.

36. Numerical assignment (hand written)
• Calculate the concentration of H+ ions in a solution of pH=0.5 ?
• Calculate the OH- ions concentration in a given solution of pH 1.1?
• Calculate the number of molecules of glucose present in 360 grams?
• Calculate the number molecules of H2SO4 in 1 mL if its of 1.84 specific gravity?
• What will be the molar volumes of NaH2PO4 and Na2HPO4 required to make a buffer
of 0.5M , if their amounts are 1.25 g and 1 g respectively used for preparing buffer.
• Calculate the amounts of acetic acid and sodium acetate, to prepare pH=7 buffer, of
0.25M and 175mL volume?pKa of acetic acid= 4.76, 96% purity of acid.
• What will be the pH of a solution containing OH- ions 1.34 x 10-4 ?
• What will be the Ka of an acid with pKa value close to 4.8?

37. What are enzymes ?  Biological catalyst
Enzymos  some catalytic agent derived from
Yeast
Catalyst is an agent that accelerates rate of the
reaction Vo by lowering the Ea (energy of activation)
without itself appearing in the products.
Ea  the energy in Cals/mol required to be
supplied to the reaction to initiate.
Both Vo and Ea are inversely proportional to each
other.
Moles of product formed per unit time is rate of
the reaction
Specificity  Absolute (1 En 1 S )and relative (1
En (range of substrates)  (gluco/hexokinases)
Mode of actions  lock and key mechanism &
induced fit model

38. Factors affecting enzyme’s activity or Vo
1. Enzyme concentration: [E] α rate of reaction Vo
• 1st order reaction  with increase of one reacting
species or factor there is proportional increase or
decrease in rate of the reaction
• Depending on hormones, metabolites, other
factors increase or decrease [E] i.e. rate of
synthesis and degradation (in hours/days)

39. Factors
2. Substrate concentration:
those following Machelis-menton kinetics
start [S] increases the Vo proportionally 1st
order reaction when substrate is less and
before Km value.

40.  Effect of temperature: within limited range i.e. due to denaturation of proteins of enzymes,
temperature increase increases Vo (Q10 principle, 30o
C valid)
• Since temperature α K.E α Vo collisions of reactants
• But maximum activity seen at each enzymes’ optimum temperature.
• Plants tolerate max at 60o
C and humans 37o
C
 Effects of pH: within limited range of pH since pH changes the ionic states of proteins which keep
them intact so certain ionic state of enzyme protein  structure + function (active site)
• But maximum activity seen at each enzyme’s optimum pH.
• Trypsin = 8-9 pH, salivary amylase= 6.4-6.9
 Effects of products: A+B  C+D (if reversible)
• Reaction may proceed more faster if products removed or reactant increased
• Reaction rate may slow if products has similarities with substrate
 Cofactors and inhibitors: cofactors (bridge S active site) and coenymes are required to make
enzyme complete and to increase rate of the reaction e.g. Fe++(cytochrome oxidase, catalase etc),
Cu++(cytochrome oxidase), Zn++ (alc. Dehydrogenase, carbonic anhydrase), Mg++(hexokinase,
pyruvate kinases etc), Mn++ (arginase), K+ (pyruvate kinases), Ni+ (urease)
• Organic or metalloorganic (group transferring)  NAD, FAD, FMN, CoASH, etc coenzymes
• Apoenzyme (protein part) cofactors (tightly bound, prosthetic groups) holoenzymes
• Inhibitors interfere

42. CLASSIFICATION OF ENZYMES
OTHLIL

43. Classification
HEXOKINASES = 2.7.1.1
(ATP; D-Glucose-6-Phosphate
Transferases
“Ase” after substrate
Lipase, urease, proteases
Machanism = transmethylase,
oxidases etc
Trivial names= No
relationship but may be latin
etc.
Pepsin, trypsin, chymotrypsin
IUBMB
4-digits + systemic name + units
i.u.= 1 umole [S][P]/min at 30o
C at opt
pH.
Katal = mole of substrate without 30o
C
More than 2 names = succinyl-coA
synthatase OR succinate thiokinases

44. Types of inhibitions of Enzymes
Reversible inhibitions
IRReversible inhibitions
IAAThiols
DIPF Acetylcholine esterases
Heavy metals (Ag+) EnZ-SH
(Mercaptides)
Ampicillin  transpeptidases (C.W)

45. Competitive enzyme inhibitions
When resemblance in structure between the
[I] and [S]
•Binds to some or all free enzymes
•Km and Vmax changes
•Lowers the [ES] complex
•Can be reversed by increasing [S]
 Important as metabolic antagonists,
chemotherapy against bacterial, viral and
malignant cancer cells
For example;
Succinate dehydrogenase
tRNA (puromycin), glutamine(azaserine), Met (ethionine)

46. In cell wall synthesis and DNA
synthesis and stops cells from dividing

48. •No resemblance with substrate
•Inhibitor doesn’t binds the active site but
sites other than active site.
•Binds to both [E] and [ES]
•Causes change in the 3-D structure of
active sites
•No effect of increasing [S]
For examples ;
1. Ions of heavy metals
2. EDTA chelates Ca++
3. Fluoride removes Mg++

49. Binds to only [ES] complex.
Makes [ESI] complexes
Not reversed by adding excess [S]
but may be by changes like pH,
temperature, etc
For example; Where two or more
substrates are required like DNA
polymerases being inhibited by
ddNTPs

50. Isozymes / iso-enzymes
Enzymes that catalyze same reaction (same
organism) but are Physically & Chemically distinct
as produced at different locations.
Lactate dehydrogenase (LDH I-V) Creatine Kinase (CK 1-3)
Each 34,000 Mol. Wt on
electrophoresis

51. Chemically distinct
LDH
2 genes seperately
encoding 2 polypeptides
(H & M types)
Combines into a 4-
polypeptides unit
LDH-1= H4 (heart), LDH-
5=M4 (skeletal muscles)
CK/CPK
2 polypeptides
B & M
Combines into Dimer
CK-1= BB (Brain), CK-
2=MB (Heart
myocardium), CK-3= MM
LDH-2 & CK-2= Myocardial Infarction in
serum appears (DIAGNOSIS)
Lungs,
kidney,
heart ,liv
er etc
Brain,
gonads,
heart ,retina,
muscles etc

52. Ribozymes
“Certain RNA molecules have catalytic properties
similar to Enzyme therefore called ribozymes”
Substrates Others RNAs or part
of ribozymes itself
Therefore believed to be first gene first enzyme evolutionary. As
in HIV viruses reverse transcriptasescDNA

53. Examples of ribozymes
1.414 bp RNA in venomes of tetra himena
catalyses self elongation from host nucleotides
2.M1-RNA in Rnase-Pprecursor t-RNA cleavge
3.RNA in self splicing of spliceosomemRNA
4.Small RNA viruses of plants
5.RNA part of rRNA in Ribosome
peptidyltransferase activity
Iron-protoporphyrin-rings  heme  Catalase
H2O2H2O + O2
Benzidine test (Blood detection)

54. Proteins
and Amino
acids