introduction to cell biology 5

1. Introduction to Cell Biology
Part 5

2. Diseases of the ER and Golgi
• Some diseases are caused by lack of signal sequence
that tells proteins to go to the ER.
– Chronic pancreatitis
– Hypoparathyroidism
• Some diseases are caused by the inability of ER to
correct misfolded proteins.
– Cystic fibrosis
– Hypothyroidism
– Albinism
– Diabetes insipidus
• Some diseases are caused by defective glycosylation.
– CDGs (congenital disorders of glycosylation)
• Some diseases are caused by defective transport of
proteins.
– Alzheimer’s disease

3. Parts of the Cell
12. Parenthesome
– Parentheses-shaped structures with unknown
composition and function
– Found only in fungal cells
13. Vesicles
– Sacs made of membrane that bud off from the ER or
Golgi apparatus
– Contains a coat that specifies which proteins are taken in
as cargo
– Transport vesicles are vesicles transferring substances
from one part of the cell to another.
– Storage vesicles are vesicles carrying substances that the
cell will store for future use.

4. Types of Vesicles
• Exosome
– Vesicles involved in exocytosis, the process of cells to
release substances to the cell exterior
– Exocytotic vesicles release substances to the cell
exterior automatically in a process known as
constitutive secretion.
– Secretory vesicles store substances near the plasma
membrane and release to the cell exterior only after
receiving a signal in a process known as regulated
secretion.
• Multivesicular body (MVB)
– Vesicle containing smaller vesicles

5. Types of Vesicles
• Endosome
– Vesicles involved in endocytosis, the process of cells to take in
substances from the cell exterior
– Vesicles involved in transcytosis, the process of cells to take in
substances from the cell exterior in one end and release the
substances to the cell exterior at the opposite end
– Pinocytosis is the process of cells to take in small substances and
liquids from the cell exterior.
– Receptor-mediated endocytosis is the process of cells to take in
substances from the cell exterior only after receiving a signal.
– Early endosomes come from either the plasma membrane or Golgi
apparatus.
– Late endosomes are early endosomes that have matured and are
more acidic than early endosomes.
• Late endosomes that originate from the plasma membrane fuse
with lysosomes to digest its contents.
• Late endosomes that originate from the Golgi apparatus fuse
with lysosomes to deliver contents.
– Recycling endosomes return to the plasma membrane.

6. Types of Vesicles
• Phagosome
– A special endosome involved in phagocytosis, the process of cells
to engulf smaller cells or food particles
• Lysosome
– Organelle made of membranous sacs filled with enzymes used for
digestion of biomolecules
– Found in animal and fungal cells but not plant cells
– Fuses with a food vacuole to digest food
– Involved in autophagy, a process of cells to recycle its own organic
material
• Fuses with a vesicle containing a damaged organelle to
degrade the organelle
– May be stained by neutral red
– Lysosomal storage diseases are due to the lysosome lacking
enzymes to digest food, causing accumulation of food particles
• Fabry disease, Tay-Sachs disease, Niemann-Pick disease, etc.

7. Types of Vesicles
• Vacuoles
– Large vesicles involved in storage of cellular products
(organic compounds, poisonous compounds, and pigments)
and breakdown of waste products
– Found in plant, protist, and fungal cells but not animal cells
– Enclosed by a membrane called tonoplast
– Gas vacuoles are hollow cavities composed of rows of hollow
cylinders covered by protein known as gas vesicles.
• Maintain buoyancy of the cells so they remain at the
appropriate depth in the water to receive sufficient amounts
of oxygen, light, and nutrients
• Found in aquatic prokaryotes
– Food vacuoles store food and originate from phagosomes.
– Contractile vacuoles pump excess water out of the cell to
maintain concentration of ions and molecules in the cell.
– Central vacuoles are made by the fusion of smaller vacuoles
and is the main repository of inorganic ions in the plant cell.

8. Parts of the Cell
14. Cytoplasmic granules
– Melanosome
• Site of synthesis, storage, and transport of melanin
• Found in animal cells
– Glyoxysome
• Found in fat storing tissues of plant seeds and fungi
• Initiates the conversion of fatty acids into sugar
– Weibel-Palade body
• Found in blood vessels and heart
– Peroxisome
• Organelle involved in removal of hydrogen atoms
• Breaks fatty acids down into smaller molecules
• Detoxifies poisonous compounds in the liver
• Produces hydrogen peroxide and converts it to water
• Diseases include Zellweger syndrome

9. Parts of the Cell
15. Cytoskeleton
– A network of fibers extending throughout the cytoplasm
involved in maintenance of cell shape and cell
movement
– Composed of proteins
– Motor proteins help the cytoskeleton move the cell.
– Microfilaments are thin and made of actin subunits.
• Functions in muscle contraction, cytoplasmic streaming, and
movement of pseudopodia
• Interacts with thick filaments of myosin in muscle cells
• Cytoplasmic streaming is a circular flow of cytoplasm.
– Intermediate filaments are made of fibrous proteins.
• Functions in nuclear lamina formation and anchorage of
organelles

10. Parts of the Cytoskeleton
• Microtubules are thick hollow tubes of tubulin molecules.
– Functions in movement of cilia and flagella and chromosome
movements during cell division
• Microtubule organizing centers (MTOCs)
– Basal body
• Anchors the cilia and flagella into the cell
• Composed of nine triplet microtubules arranged in a ring (“9+0”)
– Spindle pole body
• Found in fungal cells equivalent to the centrosome
– Centrosome
• Organelle located near the nucleus where microtubules originate
• Contains a pair of centrioles (also “9+0”) involved in cell division
• Found in animal cells but not plant and fungal cells
• Cytoskeletal diseases include Wiskott-Aldrich syndrome, Marfan
syndrome, etc.

11. Parts of the Cell
16. Undulipodium
– Hairlike appendages used for locomotion
– Composed of microtubules in a “9+2” arrangement (nine
doublets arranged in a ring with two single microtubules in
the middle)
– Dyneins are large motor proteins that help in the
movements.
– Axoneme acts as the skeleton of cilia and flagella.
– Radial spoke are T-shaped structures in the axoneme that
help the dyneins.
– Cilia are shorter and more numerous.
– Flagella are longer and fewer.
– Diseases of the cilia include polycystic kidney disease,
Bardet-Biedl syndrome, congenital heart disease, retinal
degeneration, etc.

12. Parts of the Cell
17. Proteasome
– Organelle involved in the degradation of misfolded proteins
18. Mitochondria
– Organelle where cellular respiration occurs and energy in the
form of adenosine triphosphate (ATP) is produced
– Contains a smooth outer membrane and an inner membrane
with infoldings called cristae
– Intermembrane space is the space between the outer and
inner membranes.
– Mitochondrial matrix is the space inside the inner
membrane.
– Contains its own DNA and ribosomes
– May be stained by Janus Green B
– Mitochondrial diseases include Leigh syndrome, ataxia, etc.

13. Parts of the Cell
19. Plastids
– Chromoplast
• Plant organelle involved in the synthesis and storage of pigments
– Leucoplast
• Colorless plant organelle involved in the synthesis of fatty acids and
amino acids
• Amyloplasts are involved in storing starch.
• Elaioplasts are involved in storing lipids.
• Proteinoplasts are involved in storing proteins.
– Chloroplast
• Lens-shaped green plant organelle involved in photosynthesis
• Contains two membranes with a very narrow intermembrane space
• Contains another membranous system of flattened, interconnected
sacs called thylakoids stacked together in a granum
• Stroma is the fluid inside the two membranes but outside the
thylakoids.
• Thylakoid space is the space inside the thylakoids.
• Contains its own DNA and ribosomes and chlorophyll

14. Technique: Cell Fractionation
• A cell can be separated into its different parts by
a centrifuge.
• Different speeds will sediment different parts of
the cell.
• 1000g-Nucleus
• 20000g-Mitochondria and chloroplasts
• 80000g-Plasma membrane, ER, Golgi apparatus
• 150000g-Ribosomes

15. Question
• A centrifuge has maximum speed of 50000g.
(a) Which of the cell parts can be separated?
(b)Which of the cell parts cannot be separated?

16. The Plasma Membrane

17. Plasma Membrane
• The model of the plasma membrane due to the fluidity of the
phospholipid (able to switch laterally and by flip-flopping) and
the embedding of proteins is called the fluid mosaic model.
• Cholesterol acts as a buffer to maintain the fluidity of the
plasma membrane.
• Integral proteins are embedded into the plasma membrane
and include transmembrane proteins.
• Peripheral proteins are attached loosely to the plasma
membrane.
• Glycolipids are lipids with carbohydrates attached to them.
• Glycoproteins are proteins with carbohydrates attached to
them.
• Hydrophobic molecules cross the plasma membrane easily,
but hydrophilic molecules do not cross easily, making the
plasma membrane selectively permeable.

18. Membrane Dynamics
• Hydrophilic molecules cross the plasma membrane using
transport proteins.
• Channel proteins form a tunnel in which molecules can pass.
• Aquaporins are channel proteins for water molecules.
• Ion channels are channel proteins for ionic molecules.
• Gated channels open or close in response to a signal.
• Carrier proteins change their shape whenever a molecule will
pass.
• Diffusion is the movement of any molecule to spread out
evenly in the available space.
• A substance will diffuse from a region of higher concentration
to a region of lower concentration.
• Passive transport is diffusion of a substance across the plasma
membrane because it does not require energy.
• Facilitated diffusion is diffusion across a membrane with the
help of transport proteins.

19. Membrane Dynamics
• Osmosis is diffusion of water across a selectively permeable membrane.
• Water will diffuse from a region of lower concentration to a region of
higher concentration.
• Tonicity is the ability of a solution to cause cells to lose or gain water.
• Isotonic solutions have similar concentrations with the cell and do not
cause cells to lose or gain water.
• Cells with cell walls are flaccid in isotonic solutions.
• Hypertonic solutions have higher concentrations than the cell and will
cause cells to lose water, causing the cell to shrink (if without cell wall).
• Cells with cell walls will wilt in hypertonic solutions, a phenomenon
known as plasmolysis.
• Hypotonic solutions have lower concentrations than the cell and will
cause cells to gain water, causing the cell to swell and burst (if without
cell wall) or become turgid (if with cell wall).
• Osmoregulation is the control of concentrations and water balance.

20. Question
• The cell without a cell wall contains 0.9M salt.
Describe the cell in a solution that is
(a) 0.9M salt
(b)0.3M salt
(c) 1.2M salt

21. Membrane Dynamics
• Aside from water, to move substances from lower
concentration to higher concentration will
require energy in the form of ATP, a process
known as active transport.
• Membrane potential is the voltage across a
membrane.
• Electrogenic pump is the transport protein that
generates voltage across a membrane (Na+-K+
pump for animals, H+-pump for plants, fungi, and
bacteria).
• In cotransport, a substance transported by active
transport can now diffuse back by passive
transport in exchange for the transport of
another molecule.

22. Metabolism

23. Metabolism
• Metabolism is the totality of an organism’s chemical reactions.
• A metabolic pathway involves a starting material, which is
transformed into a product by a series of steps, each step catalyzed
by an enzyme.
• Catabolic pathways degrade or break down molecules.
• Anabolic pathways synthesize or build up molecules.
• Bioenergetics is the study of how energy is produced and used up in
living organisms.
• Chemical energy is the potential energy available for release in a
chemical reaction.
• A spontaneous process occurs without the input of energy.
• Thermodynamics is the study of energy transformations that occur in
matter.
• First law of thermodynamics: Energy can be transferred or
transformed, but it cannot be created or destroyed.
• Second law of thermodynamics: For a process to occur
spontaneously, it must increase the entropy of the universe.
• Entropy is the degree of disorder of the universe.

24. Question
• The following reaction takes place: Starting
material  A C BD. If the enzymes A, B,
C, and D produce products A, B, C, and D,
respectively, make a table of the products
formed when each enzyme is defective.

25. Question
• Given that enzymes A,
B, C, and D produce
products A, B, C, and D,
respectively, and given
the table, determine
the metabolic pathway.
Defective
Enzyme
Products
Formed
A None
B A
C A, B, D
D A, B

26. Metabolism
• Exergonic/exothermic reactions release energy into the
surroundings.
• Endergonic/endothermic reactions absorb energy from the
surroundings.
• Energy coupling is the use of an exergonic reaction to drive an
endergonic reaction.
• Enzymes act as catalysts, which speed up the chemical reactions.
• Substrate is the material that an enzyme acts on. They bind to
form an enzyme-substrate complex.
• Active site is the actual site in the enzyme where the substrate
binds to.
• Induced fit allows only a specific substrate to bind to a specific
enzyme.
• The rate of enzymatic reaction increases with increasing
temperature. However, at very high temperatures, enzymes
denature because they are made of proteins.
• Cofactors are non-protein substances that help enzymes do their
work.

27. Enzyme Kinetics
• Coenzymes are cofactors that are organic.
• Enzyme kinetics is the study of the factors (temperature,
pH, presence of inhibitors) that affect the rate of enzyme
activity.
• Competitive inhibitors bind to the active site so the
substrate cannot bind.
• Noncompetitive inhibitors bind to the enzyme and change
the shape of the active site so the substrate cannot bind.
• Noncompetitive inhibition that occurs naturally is called
allosteric regulation.
• Allosteric regulation may stimulate substrate binding
instead of inhibit.
• Competitive inhibition that occurs naturally is called
feedback inhibition, where the end product binds to the
enzyme instead of the substrate.

28. Cellular Respiration
• Fermentation is the degradation of sugars without the
use of oxygen.
• Aerobic respiration is the degradation of substances
with the use of oxygen.
• Anaerobic respiration is the degradation of substances
with the use of other materials in replacement of
oxygen.
• Cellular respiration is the combination of aerobic and
anaerobic respiration.
• The general chemical equation for cellular respiration is
C6H12O6 (glucose) + 6O2  6CO2 + 6H2O + ATP (energy).
• Substrate-level phosphorylation is the formation of ATP
in glycolysis and citric acid cycle.
• Oxidative phosphorylation is the formation of ATP in
electron transport chain.

29. Redox Reactions
• Oxidation is loss of electrons.
• Reduction is gain of electrons.
• Redox reactions are a combination of oxidation and
reduction.
• The substance that becomes oxidized is the reducing
agent.
• The substance that becomes reduced is the oxidizing
agent.
• The charge of all the components must equal the
charge of the ion or chemical.
• O has a charge of -2, Group IA has charge of +1, and
Group IIA has charge of +2.
• Group VIIA may have charge of +7 or -1.

30. Question
• Give the charge of the following:
(a) Mn in KMnO4
(b)Cr in Na2CrO4
(c) Cl in HClO4
(d)I in I2
(e) C in C2O4
2-

31. Question
• Identify the oxidizing agent and reducing
agent in the following reactions:
(a) MnO4
- + I-  MnO2 + I2
(b) Cl- + Br2  Cl2 + Br-
(c) Cr2O7
2- + C2O4
2-  Cr3+ + CO2
(d) S2O3
2- + I2  I- + S4O6
2-