biochemistry notes

1. Cell and its organelles
Presented by : Rabina Ramtel
M.Sc. Clinical Biochemistry
First year
Roll no: 35

2. Outline
Introduction
History
Types of cells
Structure of cell
Cytoskeleton

3. Introduction
The cell is ultimate structural and functional unit of
body capable of performing life functions.

4. History
• Robert Hooke in 1665, discovered multitude of tiny pores
and named it “Cells”.
• In 1674, Anton Van Leeuwenhoek witnessed a live cell
under a microscope.
• In 1838, Theodor Schwann and Matthias Jacob Schleiden
summarized their observations into 3 conclusions:
 The cell is the unit of structure, physiology, and
organization in living things.
 The cell retains a dual existence as a distinct entity
and a building block in the construction of organisms.

5. Cells form by free-cell formation, similar to the
formation of crystals (spontaneous generation).
• Rudolph Virchow’s powerful dictum, ‟All cells only arise
from pre existing cells ” and promoted the third
conclusion of cell formation.

6. Modern cell theory
• All known living things are made up of cells.
• The cell is structural & functional unit of all living things.
• All cells come from pre-existing cells by division.
(Spontaneous Generation does not occur).
• Cells contains hereditary information which is passed from
cell to cell during cell division
• All cells are basically the same in chemical composition.
• All energy flow (metabolism & biochemistry) of life occurs
within cells.

7. Types of cell
1. Prokaryotic cell
2. Eukaryotic cell

9. Structure of cell
• The animal cell has three principle constituents which
are;
1. Cell membrane
2. Cytoplasm and its organelles
3. Nucleus

11. Cell wall
• Structural layer surrounding mostly prokaryotic cells except
mycoplasmas and plant cells
• Present outside the membrane
• Varies from tough to flexible and sometimes rigid
• Composition varies upon species, cell type, and
developmental stage;
- Land plants: composed of 3 layers; middle lamella, primary
cell wall and secondary cell wall.
- Bacteria : peptidoglycan
- Archaea: glycoprotein, pseudopeptidoglycan or
polysaccharides

12. - Fungi : N-acetylglucosamine polymer chitin
Function
 Helps in morphogenesis
 Provides rigidity to cells
 Create stable osmotic environment
 Permeability
 Provides protection
Extracellular matrix
• 3-D network of extracellular macromolecules such as
collagen, enzymes and glycoproteins
• Animal ECM includes interstitial matrix and basement
membrane

13. Cell membrane

14. Models of cell membrane

17. Transport across cell membrane
Three basic transport mechanism
1. Passive transport
- simple diffusion
- facilitated diffusion
2. Active transport
3. Vesicular transport
- Endocytosis
- Exocytosis

23. Channelopathies
• Disorders resulting from the abnormalities in the proteins
forming the ion channels
• Acquired and congenital
• Myasthenia gravis, liddles syndrome,

24. Cytoplasm
• Term was introduced by Rudolf von Kölliker in 1863
• Part of the cell which is contained within the entire cell
membrane, except for the cell nucleus.
• Gelatin like, semitransparent liquid consisting of 80% of
water and other substances that fills the cell.
• The main components of the cytoplasm are:
 Cytosol
 Cell organelles
 Cytoplasmic inclusions.

25. • Cytoplasm of a cell consists of two divisions:
 Ectoplasm
 Endoplasm
Functions
• Provides support and suspend organelles and cellular molecules
• Cell division (Mitosis and meiosis)
• Movement of materials
• Cyclosis
• Metabolic pathways such as glycolysis, HMP shunt pathways
occurs along with interdependance of organelles for
gluconeogenesis, heme and urea synthesis.

26. Cell organelles
Mitochondria

27. • Term coined by Carl Benda (1898)
• Mito – thread, chondrion – granule like
• Mitochondria evolved from a symbiotic relationship
between aerobic bacteria and primordial eukaryotic cells.
• Sausage shaped, spherical or oval, 0.5-1mm in diameter
• Power house of the cell
• The electron microscopic studies revealed that it has two
membranes
* Smooth Outer membrane – wrinkled and completely
surrounds the organelle.
* Inner membrane – convolutes into folds known as cristae
and contains enzymes of electron transport chain.

28. • Mitochondria contain a 16-kb circular genome (mtDNA)
that contains 37 genes criticalfor the processes of
oxidative phosphorylation.
• Thirteen of the mtDNA genes encode protein subunits of
respiratory complexes I, III, IV, and vmtDNA genome
also encodes 22 mitochondrial tRNAs and 2 rRNAs that
are essential for translation of mtDNA transcripts.

29. Functions
• Energy conversion
• Pyruvate and the citric acid cycle
• NADH and FADH2: the electron transport chain
• Storage of calcium ions
• Play a role in triggering apoptosis
• Steroidogenesis
Disorder
• Mitochondrial myopathy
• Mitochondrial encephalopathy, lactic acidosis, and stroke-like
episodes (MELAS)
• Mitochondrial DNA depletion syndrome

30. Endoplasmic reticulum

31. • First observed by Porter, Claude and Full am as an
interconnected network of tubules, vesicles and cisternae
within cells
• Present in almost all eukaryotic cells
• The most concrete hypothesis of ER is that; ER is budded
off from the nuclear envelope (Wischnitzer, 1974)
• Arise either from the outer membrane of the nuclear
envelope by folding out , or from the plasma membrane by
in folding.

32. Endoplasmic reticulum is formed of three types of elements:
− Cisternae
− Tubules
− Vesicles

33. Types of ER:
1. Rough endoplasmic reticulum (RER)
2. Smooth endoplasmic reticulum (SER)
Function of ER
− The RER is involved in:
Manufacture of lysosomal enzymes with a mannose-6-
phosphate marker added in the cis-Golgi network
provides the space and ribophorins for attachment of
ribosomes and helps in protein synthesis

34. .
− The SER is involved in:
 carbohydrate metabolism (contains the enzyme glucose-6-
phosphatase, which converts glucose-6-phosphate to glucose, a step
in gluconeogenesis)
 Steroid metabolism
 Detoxification of drugs and alcohols
 Regulates the calcium ion concentration in muscles cells
− The sarcoplasmic reticulum plays a role in excitation-
contraction coupling in muscle cells

35. Protein transport

36. − .
Disorder associated with ER
− ER dysfunction aids in a range of neurological conditions
such as alzheimer’s diseases, multiple sclerosis.
− ER storage disease; characterized accumulation of
proteins due to defect in biogenesis.
− Unfolded proteins in the lumen of ER leads to stress of
ER due to the overactivation of UPR

37. Ribosomes

38. • First observed by George Emil Palade in 1950, as a tiny
granular structures
• Serves as workbenches, with mRNA acting as blueprint in
the process of protein synthesis
• Ribosomes consist of two major components: the small
ribosomal subunits, which read the RNA, and the large
subunits, which join amino acids to form
a polypeptidechain.
• Each subunit consists of proteins(25-40%) and a type of
RNA called ribosomal RNA(37-62%).

39. Types of ribosomes
On the basis of location:
1. Membrane bound ribosomes
2. Free ribosomes or Matrix ribosomes
On the basis of sedimentation cofficient:
1. 70S ribosome
2. 80S ribosome

40. Function of ribosomes
− Protein synthesis
Disorders associated with ribosomes
− Ribosomopathies: genetic abnormalities causing
impaired ribosome biogenesis and function, resulting in
specific clinical phenotypes:
• diamond –blackfan anemia
• Treacher collins syndrome
• Cartilage –hair hypolasia
Caused by Congenital mutations in RPs19 and other genes encoding
ribosomal proteins

41. Golgi apparatus/golgi bodies

42. • 1st described by Camillo Golgi in 1898
• The subcellular localization of the Golgi apparatus varies
among eukaryotes.
• In mammals, a single Golgi apparatus is usually located
near the cell nucleus, close to the centrosome.
• Clusters of flattened membrane vesicles called
dictyosomes(cisternae) which are connected to one another
constitute a golgi complex.
• Collection of cisternae is broken down into cis, medial,
and trans compartments and make up two main networks:
 Cis Golgi Network (CGN)
 Trans Golgi Network (TGN).

43. • The compartmentalization of the Golgi apparatus is
advantageous for assortments of enzymes responsible for
selectively modifying protein cargo and maintaining
consecutive and selective processing steps such as:
− enzymes catalyzing early modifications are gathered in
the cis face cisternae.
− enzymes catalyzing later modifications are found in trans face
cisternae of the Golgi stacks
Functions
• major collection and dispatch station of protein products
received from the ER.
• Lipid transport and lysosome formation.

44. • Post-translational modification of proteins.
For example:
 phosphorylation of oligosaccharides on lysosomal
proteins occurs in the early CGN
 addition of carbohydrates (glycosylation) and phosphates
(phosphorylation).
• formation of proteoglycans

45. Disorders
• Defect in the microtubules of the Golgi apparatus leads to
achondrogenesis type 1A
• Pelizaeus-Merzbacher disease in which, mutant
PLP1(proteolipid protein 1) is misfolded and accumulates
in the ER, which in turn inhibits Golgi-to-ER retrograde
trafficking.
• Proximal spinal muscular atrophy in which there is loss
of expression of SMN1( survival motor neuron 1) along
with a global blockade of granule export from the trans-
Golgi network resulting in accumulation of granules.

46. Lysosomes

47. • 1st described by christian de Duve in 1950.
• Spherical vesicles bounded by a single membrane
• 1µm diameter
• Packets of hydrolysing enzymes known as lysozymes
• Contain more than 60 different enzymes, and have more
than 50 membrane proteins.
• Cathepsins are the major class of hydrolytic enzymes,
• lysosomal alpha-glucosidase is responsible for
carbohydrates,
• lysosomal acid phosphatase is necessary to release
phosphate groups of phospholipids.

48. Formation of lysosomal enzymes
• Enzymes of the lysosomes are synthesised in the RER.
• Enzymes are imported from the Golgi apparatus in
small vesicles, which fuse with larger acidic vesicles.
• Enzymes destined for a lysosome are specifically
tagged with the molecule mannose 6-phosphate, so that
they are properly sorted into acidified vesicles

49. Formation

50. Function of lysosomes
• Intracellular digestion
• Removal of dead cells
• Role in metamorphosis
Disorders
- Mutations in the genes responsible for synthesis of lysosomal
enzymes results in more than 30 different human genetic
disorders, which are collectively known as lysosomal storage
diseases
• such as Gaucher's disease; deficiency of the
enzyme glucocerebrosidase.

51. • In gout, urate crystals are deposited around knee
joints which when phagocytosed cause physical
damage to lysosomes and relases enzymes leading to
inflammation and arthritis
• inclusion cell disease

52. Peroxisomes

53. • Identified as organelles by the Belgian cytologist Christian de
Duve in 1967 after they had been first described by a Swedish
doctoral student, J. Rhodin in 1954.
• It is a microbody of about 0.3-1.5mm in daimeter
• Made up of phospholipid bilayer with many membrane bound
proteins

54. Function
− Consists of peroxidases and catalase that is associated with
lipid metabolism and processing of reactive oxygen species
− First reactions in the formation of plasmalogen in animal cells
occur in peroxisomes
− Also play a role in the production of bile acids important for
the absorption of fats and fat-soluble vitamins
Disorder associated with peroxisomes
− Defect in peroxisome biogenesis
− X-linked adrenoleukodystrophy

55. Nucleus

56. • Discovered by Robert Brown in 1831
• Average diameter of 6µm and occupies about 10% of cell
volume
• Components of nucleus:
- nuclear envelope
- nuclear membrane
- nucleolus
- chromosomes
- nucleoplasm

57. Functions of nucleus
− It is like the brain in a cell and controls the cell activities
such as growth, metabolism, protein synthesis, cell
movement and actions.
− Stores genetic information (DNA and RNA)
− Selective transportation of regulatory factors and energy
molecules through nuclear pores
Disorder associated with nucleus
− Striated muscle diseases
− Lipodystrophy syndromes
− Pheripheral nerve disorders
− Bone diseases

58. cytoskeleton

59. • Stable and dynamic network of protein fibres that gives
the cell shape and structure, organizes the cytoplasm and
produces motion
• Types of cytoplasmic filaments are:
- Microfilaments made up of actin
- Intermediate filaments
- Microtubules (tubulin proteins)
- Molecular motors

60. References
• Lehninger-Principles of Biochemistry 5th edition
• Becker,W.M., Kleinsmith, L.J., Hardin, J., and Bertoni, G.P., The
World of the Cell (7th ed.), Benjamin Cummings (2009). [A
highly readable cell biology text.]
• Martin WF, Müller M (2007). Origin of mitochondria and
hydrogenosomes. Heidelberg: Springer Verlag.
• McBride HM, Neuspiel M, Wasiak S (July 2006). "Mitochondria:
more than just a powerhouse". Current Biology
• Wanders RJ, Waterham HR (2006). "Biochemistry of mammalian
peroxisomes revisited". Annual Review of Biochemistry.

61. • Lodish H, et al. (2003). Molecular Cell Biology (5th ed.).
W. H. Freeman. pp. 659–666. ISBN 978-0-7167-4366-8.
• Cooper GM (2000). The cell: a molecular approach (2nd
ed.). Washington (DC): ASM Press. ISBN 978-0-87893-
106-4. Archived from the original on 2014-03-11
• de Duve C (Apr 1969). "The peroxisome: a new
cytoplasmic organelle". Proceedings of the Royal Society
of London. Series B, Biological Sciences. 173 (1030):
71–83. doi:10.1098/rspb.1969.0039. PMID 4389648

62. • Davidson MW (2004-12-13). "The Golgi
Apparatus". Molecular Expressions. Florida State
University. Archived from the original on 2006-11-07.
Retrieved 2010-09-20.
• Saftig P, Klumperman J (September 2009). "Lysosome
biogenesis and lysosomal membrane proteins: trafficking
meets function". Nature Reviews Molecular Cell
Biology. 10(9): 623–
35. doi:10.1038/nrm2745. PMID 19672277

63. Thank you….