Biochemistry •

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Biological Molecules

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Carbohydrates

Significance of Biochemistry

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Characteristics of Living Organisms Proteins

Biological Molecules

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 Origins of Biochemistry

Pioneers

Lipids

Nucleic Acids
Distinctive Properties of Living Systems

The Biggest Biological Distinction of Prokaryotes

and Eukaryotes
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Cell City
Viruses
Membrane Lipids
- phospholipids, glycolipids, cholesterol
- form bilayer in aqueous medium, burying their
hydrophobic tails and leaving their hydrophilic ends
exposed to the water

Membrane Proteins
- Integral Proteins
>> are either partially or totally immersed in the lipid
bilayer
>> span the lipid bilayer from one side to the other
and are called transmembrane protein
- Transmembrane Proteins
>> act as enzymes and transport carriers for ions as
well as water soluble substances, such as glucose
- Peripheral Proteins
>> attached to the surface of the lipid bilayer by
electrostatic and hydrogen bonds.

Membrane Carbohydrates
- occurs in combination with proteins or lipids in the
form of glycoproteins or glycolipids.

Biological membranes
- are semipermeable membranes through which
certain molecules freely diffuse across membranes, but
the movement of the others is restricted because of
size, charge or solubility.
Particles - Carrier Protein is capable of transporting substance
against the concentration gradient

Passive Transport or Passive Diffusion

- the process by which molecules move across a
membrane without energy (ATP)
- direction: always from a region of higher
concentration to one of lower concentration

Active Transport
Pinocytosis
- molecule moves against a concentration gradient, an
- only process by which most macromolecules
external energy source is required
(proteins, polysaccharides, polynucleotides) can enter
- substances: Na+, K+, Ca++, H+, Cl-, sugars and most
cells
of the amino acids
- These molecules first attach to a specific receptors.
- 2 types (according to the source of energy used)
>>Receptors are coated on the cytoplasmic side with
1. Primary Active Transport
a fibrillar protein “calthrin” and contractile filaments
2. Secondary Active Transport
of “actin and myosin”
- depends on the carrier proteins like facilitated
diffusion
- Once the macromolecules (which is to be absorbed)
have bound with the receptors, the entire pit
invaginates inward, and the fibrillar protein by
surrounding the invaginating pit causes it to close over
the attached macromolecule along with a small
amount of extracellular fluid
- Then immediately, the invaginated portion of the
membrane breaks away from the surface of the cell
forming --
Endocytosis
- Pinocytosis (Cell drinking)
- Phagocytosis (Cell eating)
Phagocytosis
- involves ingestion of large particles (viruses,
backteria, cells, tissue debris or a dead cell)
- occurs only in specialized cells (macrophages and
some of the WBCs
Exocytosis
- most of the endocytic vesicles formed from
pinocytosis fuse with lysosomes.
>> Lysosomes empty their acid hydrolases to the
inside of the vesicle and begin hydrolyzing the
proteins, carbohydrate, lipids and other substances in
the vesicle
- the macromolecular contents are digested to yield
amino acids, simple sugars or nucleotides and they
diffuse out of the vesicle and reused in the cytoplasm
- undigestible substance “residual body” is finally
excreted through the cell membrane by a process
called exocytosis
- the undigestible substances produced within the
cytoplasm may be enclosed in membranes to form
vesicles called “exocytic vesicles”
>>fuse with the internal surface of the internal
membranes
>> then, ruptures releasing their contents into the
extracellular space and their membranes are retrieved
- cells release large molecules from cells to the
outside
Enzymes
- catalysts that increase the rate of a chemical reaction
without being changed themselves in the process.
- in the absence of an enzyme, the reaction may hardly
processed at all, whereas, in its presence the rate can
be increased up to 10*7 fold.
- often show substrate specifically by limiting their
action to one substance or a small number of
structurally related substances
- the properties and spatial arrangement of the amino
acid residues forming the active site of an enzyme will
determine which molecules can bind and be substrates
for that enzyme.
- the active site of an enzyme is the region that binds
the substrate and converts it into product
- Isoenzymes are different forms of an enzyme which
catalyze the same reaction, but which exhibit different
physical or kinetic properties.
- Organisms are 70 – 90% water.
- Normal metabolic activity can occur only when cells
are at least 65% H2O
- Hydrogen Bonding in water is the key to its properties:
ability of water to form hydrogen bonds
-Molecular interactions in liquid water are based on H
Bonds
- Solvent Properties of Water derive from its polar
nature
- Water can ionize to form H+ and OH-
Water: The Solvent of Biochemical Reactions
- Water and Polarity
- Hydrogen Bonds
- Acids, Bases and pH
- Buffers
Water and Polarity
- Terms
>> Electronegativity – measure of the tendency of
an atom to attract electrons to it in a chemical bond
>> Polar Bonds – 2 atoms have an unequal share in
the bonding electrons
>> Nonpolar – bond in which two atoms share
electrons evenly
>> Dipoles molecules – with positive and negative
ends due to an uneven distribution of electrons in
bonds
>> Hydrophilic – dissolve in water
>> Hydrophobic – tending not to dissolve in water
>> Amphiphatic – molecule that has one end with a
polar, water-soluble group and another end with a
nonpolar hydrocarbon group that is insoluble in water
Acids, Bases , and pH
pH
- Soren Sorensen, Danish biochemist, devised pH scale
by defining pH as the negative logarithm of the
hydrogen ion concentration
- pKw = pH + pOH = 14
Acid
- a biologically useful definition of an acid is a molecule
that acts as a proton (hydrogen ion) donor
- also known as Bronsted acid in strict chemistry.
Base
- similarly defined as a proton acceptor.
Acids and Bases
- useful to derive a numerical measure of acid strength
>> amount of hydrogen ion released when a given
amount of acid is dissolved in water.

Hydrogen Bonds
- water has an unrivaled ability to form hydrogen Henderson-Hasselbatch Equation
bonds in the crucial fact to understanding its - provides a general solution to the quantitative
properties. treatment of acid-base equilibria in biological systems
- has 2 hydrogens to enter into hydrogen bonds and 2 - a mathematical relationship between pKa of an acid
unshared pairs of electrons on the oxygen to w/c and the pH of a solution containing the acid and its
other water molecules can be hydrogen-bonded. conjugate base.
- Ice has a lower density than liquid water bc the fully
hydrogen bonded array in an ice crystal is less packed
than that in liquid water.
>> Liquid water is less extensively hydrogen-bonded
and thus is denser than ice. Thus, ice cubes and
icebergs float
- In liquid water, hydrogen bonds are constantly
breaking and new ones are constantly forming, with
some molecules breaking off and others joining the
cluster.
Buffers
- solutions that tend to resist changes in their pH as acid
or bases is added
- buffer system is composed of a weak acid and its
conjugate base