PENGANTAR BIOKIMIA UMUM

Lina Nafisah, M.Farm

 Buku Referensi
• Biochemistry, 6th Edition (Lehninger)
• Harper Biochemistry, Edisi 26 (Robert K.
Murray et al.)
 PENGERTIAN BIOKIMIA
• BIOKIMIA : ilmu yang berhubungan dengan berbagai
molekul di dalam sel atau organisme hidup sekaligus
dengan reaksi kimia yang terjadi di dalamnya.
BIOS CHEMIOS

HIDUP/HAYATI KIMIA/SENYAWA
ORGANIK

KIMIA
BIOLOGI ORGANIK

ILMU KIMIA HAYATI (BIOKIMIA)

Cell: The Universal Building Block
• Living organisms are made of cells
• Simplest living organisms are single-celled
• Larger organisms consist of many cells with different
functions
• Not all of the cells are the same
All cells share some common features
Three Distinct Domains of Life Defined
by: Cellular and Molecular Differences
 Six Kingdoms of Life Defined by:
Organism, Cellular, and Molecular Differences

Six kingdoms Cellular organization

• Archaea Unicellular prokaryote
• Bacteria Unicellular prokaryote
• Protista Unicellular eukaryote
• Fungi Uni- or Multicellular eukaryote
• Plantae Multicellular eukaryote
• Animalia Multicellular eukaryote
Bacterial Cell Structure
 Components of Bacterial Cell

Structure Composition Function

Cell wall Peptidoglycan Mechanical support
Cell membrane Lipid + protein Permeability barrier
Nucleoid DNA + protein Genetic information
Ribosomes RNA + protein Protein synthesis
Pili Protein Adhesion, conjugation
Flagella Protein Motility
Cytoplasm Aqueous solution Site of metabolism
 Eukaryote Cells: More Complexity
• Have nucleus by definition
– protection for DNA; site of DNA metabolism
– selective import and export via nuclear membrane pores
– some cells become anuclear (red blood cells)
• Have membrane-enclosed organelles
– Mitochondria for energy in animals, plants, and fungi
– Chloroplasts for energy in plant
– Lysosome for digestion of un-needed molecules
• Spatial separation of energy-yielding and energy-
consuming reactions helps cells to maintain
homeostasis and stay away from equilibrium
Hirarki organisasi molekul dalam sel, pada sel tumbuhan ini
nukleus merupakan organel yang mengandung beberapa tipe
kompleks supramolekul, termasuk kromosom, kromosom terdiri
dari makromolekul DNA dan sejumlah protein. DNA dan protein
disusun oleh unit monomer.
 2 | Water and Aqueous Solutions

© 2013 W. H. Freeman and Company

© 2013 W. H. Freeman and Company

 Water is the medium for life

• Organisms typically contain 70–90% water

• Chemical reactions occur in aqueous

• Water is a critical determinant of the

structure and function of proteins, nucleic
acids, and membranes
 Water as a Solvent
• Water is a good solvent for charged and polar
substances
– amino acids and peptides
– small alcohols
– carbohydrates
• Water is a poor solvent for nonpolar substances
– nonpolar gases
– aromatic moieties
– aliphatic chains
 Water dissolves many salts

• Tingginya konstanta dielektrik air akan

menyebabkan berkurangnya tarik-menarik ion
yang berlawanan pada garam, sehingga hampir
tidak ada interaksi pada jarak yang jauh (> 40 nm)
• Tingginya interaksi elektrostatik antara ion yang
terlarut dengan mulekul air akan menurunkan
energi sistem.
 Physics of Noncovalent Interactions
Noncovalent interactions do not involve sharing a pair of electrons. Based on their
physical origin, one can distinguish between:

• Ionic (Coulombic) Interactions

– Electrostatic interactions between permanently charged species, or
between the ion and a permanent dipole
• Dipole Interactions
– Electrostatic interactions between uncharged, but polar molecules
• van der Waals Interactions
– Weak interactions between all atoms, regardless of polarity
– Attractive (dispersion) and repulsive (steric) component
• Hydrophobic Effect
– Complex phenomenon associated with the ordering of water
molecules around nonpolar substances
Examples of Noncovalent Interactions
 Importance of Hydrogen Bonds
• Source of unique properties of water
• Structure and function of proteins
• Structure and function of DNA
• Structure and function of polysaccharides
• Binding of substrates to enzymes
• Binding of hormones to receptors
• Matching of mRNA and tRNA
“I believe that as the methods of structural chemistry are further applied to
physiological problems, it will be found that the significance of the hydrogen bond
for physiology is greater than that of any other single structural feature.”
–Linus Pauling, The Nature of the Chemical Bond, 1939
Hydrogen Bonds: Examples
Biological Relevance of Hydrogen Bonds
 van der Waals Interactions
• van der Waals interactions have two
components:
– Attractive force (London dispersion) depends on
the polarizability
– Repulsive force (Steric repulsion) depends on the
size of atoms
• Attraction dominates at longer distances
(typically 0.4–0.7 nm)
• Repulsion dominates at very short distances
• There is a minimum energy distance (van der
Waals contact distance)
 Biochemical Significance of
van der Waals Interactions

• Weak individually
– easily broken, reversible
• Universal
– occur between any two atoms that are near each
other
• Importance
– stabilizes biological macromolecules (stacking in
DNA)
– facilitates binding of polarizable ligands
 The Hydrophobic Effect
• Refers to the association or folding of
nonpolar molecules in the aqueous solution
• Is one of the main factors behind:
– protein folding
– protein-protein association
– formation of lipid micelles
– binding of steroid hormones to their receptor
Solubility of Polar and Nonpolar Solutes

Why are nonpolar molecules poorly soluble in water?

 What is pH?
• pH is defined as the negative
pH = -log[H+] logarithm of the hydrogen ion
concentration
• Simplifies equations
K w  [H  ][OH- ]  1 10 14 M 2 • The pH and pOH must always
add to 14
 log[ H  ]  log[OH- ]  14 • In neutral solution, [H+] = [OH–]
and the pH is 7
pH  pOH  14 • pH can be negative ([H+] = 6 M)
pH scale is logarithmic:
1 unit = 10-fold
pH of Some Common Liquids
 pKa measures acidity
• pKa = –log Ka (strong acid  large Ka  small pKa)
 Buffers are mixtures of weak acids and their
anions (conjugate base)
• Buffers resist change in pH

• At pH = pKa, there is a 50:50 mixture of acid and

anion forms of the compound

• Buffering capacity of acid/anion system is greatest

at pH = pKa

• Buffering capacity is lost when the pH differs from

pKa by more than 1 pH unit
Acetic Acid-Acetate as a Buffer System
Weak acids have different pKas
 Biological Buffer Systems
• Maintenance of intracellular pH is vital to all cells
– Enzyme-catalyzed reactions have optimal pH
– Solubility of polar molecules depends on H-bond donors and acceptors
– Equilibrium between CO2 gas and dissolved HCO3– depends on pH

• Buffer systems in vivo are mainly based on

– phosphate, concentration in millimolar range
– bicarbonate, important for blood plasma
– histidine, efficient buffer at neutral pH

• Buffer systems in vitro are often based on sulfonic acids of cyclic

amines
– HEPES
HO
– PIPES N N
– CHES SO3 Na
Water as a Reactant in Biochemistry
Terima Kasih