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Concepts of Biochemistry
Biochem-700

Dr. Nayla Munawar

Assistant professor
Department of Biochemistry
UAF

Cell
Cell is structural and functional unit of all living organisms

Definition: Any of the protoplasmic mass making up organized tissue

consisting of a nucleus and the cytoplasm surrounding the nucleus.

Nucleus is separated from cytoplasm by nuclear membrane (nuclear

envelop)

Cytoplasm is surrounded by plasma membrane

Eukaryotes (eu=true; karyo=nucleus): Unicellular or multicellular

organisms with cell(s) having a membrane bounded nucleus

Prokaryotes (pro=before; karyo=nucleus): Unicellular organisms with

a single chromosome without a true nucleus, the genetic material
being scattered in the cytoplasm

Structurally it consist of an aggregation of molecules that enabling the

survival and growth of the whole organism

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Molecules in the cell composed chemically from nucleic acids,

proteins, carbohydrates and lipids

Synthesis and breakdown of these molecules are located in

certain organelles
These organelles are:

u Nucleus
v Ribosomes
² Endoplasmic reticulum
q Mitochondria
ü  Golgi bodies
o  Lysosomes
Ø  Cytoskeleton

Eukaryotic cells:
þ  Animal
þ  Plant

Prokaryotic cells:
¤  Bacteria
¤  Archaea
¤  Cyanobacteria

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Summary of differences!
Prokaryotic Cells
small cells (< 5 mm)
always unicellular
no nucleus or any membrane-bound
organelles
DNA is circular, without proteins
ribosomes are small (70S)
no cytoskeleton
cell division is by binary fission
reproduction is always asexual
Nucleus
Structure
1.  It is surrounded by lipid bilayer
perinuclear envelop (nuclear membrane
or karyotheca)
2.  Rich in DNA and RNA
3.  DNA combines with histones and
organized into chromosomes
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Eukaryotic cells
larger cells (> 10 mm)
often multicellular
always have nucleus and other
membrane-bound organelles
DNA is linear and associated with
proteins to form chromatin
ribosomes are large (80S)
always has a cytoskeleton
cell division is by mitosis or meiosis
reproduction is asexual or sexual
Functions
1. During mitosis, chromosomes
undergo replication of their DNA and
separation into daughter
chromosomes
2. DNA directs the protein
biosynthesis inside the cell
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Cytosol

Composition Function

ü  It is the soluble fraction of the ²  Most of the proteins of the cytosol

cytoplasm are enzymes required in metabolism

ü  It is highly viscous ²  Cytosol also contains metabolic

ü  The protein concentration is more intermediates and inorganic salts

than 20%

Ribosome

Composition Function

q  Each ribosome has a large and small u  Ribosomes are the sites of protein
subunit. synthesis
q  Eukaryotic cell ribosomes (60S and u  Free ribosomes make proteins used
40S) by the cell
q  Prokaryotic cell ribosomes (50S and u  Ribosomes on rER make proteins for
30S) export to other cells
q  Each subunit consists about 65%
RNA and 35% protein
q  Ribosomes are either free in the
cytoplasm or attach with
endoplasmic reticulum (rER)
q  No membrane

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Smooth and rough endoplasmic reticulum

Composition Function

-The endoplasmic reticulum consists -Rough endoplasmic reticulum is a site

of flattened, single membrane for protein biosynthesis
vesicles, whose inner compartments
the cisternae, interconnected to form -Smooth endoplasmic reticulum is a site
channels throughout the cytoplasm for lipids synthesis

-Rough endoplasmic reticulum

contain ribosomes on its surface

Golgi apparatus

Composition Golgi apparatus functions in:

v  It consists of flattened, single
1.  Packing the proteins synthesized in
membrane vesicles.
ribosomes
v  Some become vacuoles in which
2.  Addition of non-protein fragment to
secretory products are concentrated proteins e.g. addition of carbohydrate to
protein to form glycoproteins and
addition of zinc to proinsulin to form the
active hormone
3.  H e l p s t h e f o r m a t i o n o f p l a s m a
membrane of lysosomes
4.  Golgi apparatus functions in the
secretion of cell products such as
proteins to outside the cell

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Mitochondria

Function
Composition
«  The mitochondria are the power
­  There are about 800 mitochondria in the
houses of the cell
liver cell
«  Carbohydrates, lipids and amino
­  Their outer and inner membranes differ
acids are oxidized to CO2 and
in lipids composition and enzymatic
H2O by molecular O2
activity
«  The energy liberated is stored in
­  Matrix is rich in enzymes
ATP molecule
«  The enzyme of electron transport,
energy liberation and ATP
formation are located in the inner
membrane

Peroxisome

Composition Function

①  M i c r o b o d i e s , a r e s i n g l e A.  Peroxisomes share in the oxidation of

membrane vesicles. certain nutrients
②  They contain enzymes like B.  Hydrogen peroxide (H2O2) is
catalase, D-amino acid oxidase converted into H2O and O2 in
and other oxidative enzymes peroxisomes

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Lysosomes

Composition Function

•  Lysosomes are single membrane §  Lysosomes function in the digestion of

vesicles. materials brought into cell by
•  They contain hydrolytic enzymes phagocytosis or pinocytosis
such as ribonulease and §  T h e y a l s o s e r v e t o d i g e s t c e l l
phosphatase components after cell death

Storage granules

Function
Composition
u  When needed as fuel, these
Ø  These are polymers of sugars
polymers are enzymatically
degraded to yield free glucose or
Ø  Some bacteria contain granules of
free β-hydroxy butyric acid
poly-β-hydroxy-butyric acid

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Cell membrane

Membranes are semi permeable and

mainly formed of

①  Lipids
②  Proteins
③  Carbohydrates

-Lipids (mainly phospholipids, glycolipids, cholesterol)

Lipid bilayer membranes: In aqueous solution, membrane phospholipids are

arranged in bilayer form where the polar groups are arranged outside, while
nonpolar groups are arranged inside

Stability of lipid bilayer: Hydrophobic interaction (major force); Van der Waals
attractive forces; Electrostatic and hydrogen bonding.
-
Functions: Fluidity and selective permeability

Proteins (Peripheral and integral membrane proteins)

Peripheral membrane proteins

-Weakly bound to surfaces of integral membrane proteins
-Can be removed by salt solution without disturbing membrane
Integral membrane (transmembrane proteins)
-Deeply embedded in the lipid bilayer
-Attached by Van der Waals forces and removed by detergent
Function: serve as transporters including energy dependent pumps,
pores, gates, receptors, energy transducers and enzymes

-Carbohydrates (glycoproteins and glycolipids)

Present in the form of glycoproteins and glycolipids
Located at the external surface of cell membrane
Function: reporters in the form of glycoprotein

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Fluid-Mosaic Model
Describes the plasma membrane of the animal cells

Plasma membrane has two layers of phospholipids (fats with phosphorous

attached) which at body temperature are like vegetable oil (fluid)

Each phospholipid has hydrophilic head (pointing toward outside) and

hydrophobic tail (forms the inside of the bilayer)

Proteins and substances such as

cholesterol become embedded in the
bilayer giving the membrane the look of
“mosaic”.

Fluid-Mosaic Model
Plasma membrane has consistency of oil at body temperature and proteins
and substance are able to move across it so it described using fluid-mosaic
model

Embedded molecules in plasma membrane serve a purpose

Cholesterol: make membrane more stable

Prevent it from solidification at low body temperature

Carbohydrate chains: attaches to the

outer surface of the plasma membrane

Specific to every person and supply

characteristics such as blood group

Proteins: serve as transporters

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Function of cell membrane

Transfer of small molecules

1.  Passive (simple) diffusion Passive
2.  Facilitated diffusion or Carrier mediated diffusion transport

3.  Osmosis
4.  Active transport

Transfer of large molecules

1.  Endocytosis
2.  Exocytosis

Transfer of small molecules

1. Passive (simple) diffusion

i.  Substances move from higher to lower concentration
ii.  No need of energy
iii.  Rate of transport depends on the solubility of transported molecules in the
hydrophobic core of the membrane
Transmembrane channels (protein containing pores)
They transport several species of similar size and charges e.g. Na+ and K+
Some channels are open continuously other (Ca++ channels open only in
resonance to some signals (gated channels)

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2. Facilitated diffusion or Carrier mediated diffusion

-Transport of small molecules by specific carrier proteins e.g. glucose carrier
proteins (GLUT4), amino acid carrier proteins
-Facilitated diffusion can be saturated (diffusion stops when all carrier proteins
are saturated with transported molecules “Pong” “Ping”

-Ping pong model of facilitated diffusion

Carrier proteins can exists in 2 configurations: ping and pong
Factors affecting facilitated diffusion:
Ø  Amount of carrier proteins
Ø  Affinity of he transported molecules to the carrier proteins
Ø  Rapidity of conformational changes
Ø  Hormones e.g. insulin increases the glucose carrier proteins

3. Osmosis

cells can gain or loss water by the process called osmosis

Definition: The net movement of water from a region of high concentration to

the region of low concentration through a semipermeable membrane
Osmosis is a special case of diffusion
Diffusion of water across a selectively permeable membrane (a barrier that
allows some substances to pass but not others). The cell membrane is
such a barrier.

Small molecules pass through – e.g.

water
Large molecules can’t pass through – e.g.
proteins and complex carbohydrates

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Cytoplasm is a solution of water and solids (solutes dissolved in the water).

Water moves into and out of cells because of the different concentration
of the solutes.
Different kinds of cells react differently depending on the solution they
are in.

Hypotonic – comes from Greek “hypo” meaning “under” and “tonos” meaning
“stretching”
The solution on one side of a membrane where the solute concentration is less
than on the other side. Hypotonic Solutions contain a low concentration of
solute relative to another solution.

Hypertonic – comes from Greek “hyper” meaning over and “tonos”

meaning “stretching”
The solution on one side of a membrane where the solute concentration is
greater than on the other side. Hypertonic Solutions contain a high
concentration of solute relative to another solution.

Hypertonic environment such as concentrated brines or syrups have been used

for food preservaDon

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Isotonic- The root word iso means “equal”. If you remember hypertonic
and hypotonic are higher and lower concentrations then isotonic must be
the case where both solutions have equal concentration.

Over time molecules will move across the membrane until the concentration
of solutes is equal on both sides. This type of solution is called ISOTONIC.

A 0.9% solution of NaCl is isotonic to animal cells

Significance of passive transport to living cells

1.  Passive transport occurs without expenditure of energy.

2. Molecules move using their own kinetic energy .

Diffusion and osmosis are examples of passive transport.

3. Passive transport allows cells to get water, oxygen and other small
molecules that they need.

4. It also allows the cell to get rid of waste such as carbon dioxide.

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4. Active transport

Substance move from lower concentration to higher concentration

Needs energy (sodium-potassium pump) by the hydrolysis of ATP in the

presence of ATPase enzyme

Na+ K+ ATPase of cell membrane (Na+ K+ pump)

Extracellular fluid has higher concentration of Na+ than the intracellular

fluid while K ion concentration is opposite to that of Na+ ions

Antiporter pump of Na+ K+ ATPase in the efflux of 3Na+ ions and

simultaneous influx of 2K+ ions across the cell membrane

Energy is provided by hydrolysis of ATP using ATPase (transmembrane

integral protein which differ in different tissues

Each turnover of the pump transfers one net positive charge out of the cell

This makes cell membrane negatively

charged on its interior and positively
charged on its exterior

Therefore, pump is called electrogenic

pump

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B. Transfer of large molecules

1.  Endocytosis:

i.  Pinocytosis (cell drinking)

Occurs in all cells and leads to cellular uptake of fluid.
Liver uptake chylomicrons and LDL by pinocytosis

ii. Phagocytosis (cell eating)

Occurs only in specialized cells, macrophages and
granulocytes as they ingest bacteria

2. Exocytosis
It is used to release macromolecules made in the endoplasmic reticulum and golgi
apparatus to the out side of the cell e.g. release of insulin hormone from β-cells of
islets of Langerhans in pancreas

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