Transcript Living Organisms - Bilkent University

Living Organisms
Living systems are separated from
other chemical systems by;
• The capacity for replication;
• The presence of enzymes and other complex
molecules;
• A membrane that separates the internal
chemicals from the external chemical
environment.
Terms applied to cells
• Heterotrophs (other-feeder): an organism that
obtains its energy from another organism.
Animals, fungi, bacteria, and many protistans
are heterotrophs.
• Autotrophs (self-feeder): an organism that
makes its own food, it converts energy from an
inorganic source in one of two ways
• Photosynthesis is the conversion of
sunlight energy into C-C covalent bonds of
a carbohydrates. This led to the oxidative
metabolism
• Chemosynthesis is the capture of energy
released by certain inorganic chemical
reactions.
Time scale of Evolution
• Life emerged at least 3.8
billion years ago.
• Simple organic molecules
could form and
spontaneously polymerize
into macromolecules.
• No free oxygen but
consists CO2 and N2.. Also
small amount of H2, H2S
and CO.
• RNA world-self replicating
RNA molecules.
Evolution of cells
From the Cell, A Molecular Approach
2nd edition; Cooper; ASM Press & Snauer
4.2 Cell sizes vary with their function
• Below is a list of the most common units of
length biologists use (metric)
Table 4.2
• Cell size and
shape relate
to function
Figure 4.2
Why cell size vary?
• Smallest cells:
– Mycoplasmas; they have the smallest genome
• Bulkiest cells:
– Bird eggs, young need a lot of food
• Longest cells:
– Nerve cells, can transmit signals over long
ranges
What limits cell size?
• Lower limits
– What does the cell need to contain?
• Must house DNA, proteins, and organelles (in
eukaryotes).
• Upper limits
– It must have enough surface area, why?
• Must be able to obtain enough nutrients from the
environment.
Prokaryotic Cells
• Archaebacteria
• Eubacteria
• They have plasma membrane
• They have nucleoid
• They have cytoplasm with ribosomes
Prokaryote (pro=before,
karyo=nucleus)
From Life: The Science of Biology,
4th Edition Sinauer & WH Freeman
Prokaryotic cells
•
•
•
•
Very diverse in their metabolic capabilities.
Some archae are found in hot springs
Some of them are photosynthetic.
Some are able to oxidize inorganic ions to
obtain energy
• prokaryotes are asexual, meaning their
offspring nearly always bear the exact
characterisics of the parent cell. Division
is by binary fission.
Prokaryotic cells
• Prokaryotic DNA is organized as a
circular chromosome.
• DNA is supercoiled
• Most of DNA is protein coding
Prokaryotes
• In Greek pro means before and karyon refers to
nucleus.
• Nucleoid(=nucleus like), coiled DNA of a prokaryote.
• No organelles in prokaryotes.
• Ribosomes (that assemble amino acids) are free in
cytoplasm.
• Cell membrane surrounds the cell; cell wall protects
the cell. In some, there is a sticky coat called a capsule
(works like a glu).
• Pili and flagella are for attachment and movement.
Procaryote sizes and structures
From Molecular Biology of the Cell
Third edition; Alberts; Garland
Schematic diagram of a typical prokaryotic cell.
Specialized features of some
prokaryotes-1
• Cell wall: Outside
the PM. Supports
the cell and
determines the
shape.
• It contains
peptidoglycan.
• It is not a barrier
and some toxins
can cause disease
From Life: The Science of Biology,
4th Edition Sinauer & WH Freeman
Specialized features of some
prokaryotes-2
• Capsule:
• It encloses cell wall
and outer
membrane.
• It may protect
from WBC
• It is not necessary
for living
Specialized features of some
prokaryotes-3
• Mesosome:
• It is formed by
infolding of the PM
• It may aid the
movement in & out
of the cell of
materials. It may
also aid the
replication of DNA
and cell division.
Specialized features of some
prokaryotes-4
• Flagella
• Bacterium moves
with its help
• It is anchored
to the PM and
cell wall
Specialized features of some
prokaryotes-5
• Pili
• projected from
the surface
• helps to adhere
to another
bacteria
• shorter than
flagella
From the Cell, A Molecular Approach
2nd edition; Cooper; ASM Press & Snauer
Structures of animal cells
From the Cell, A Molecular Approach
2nd edition; Cooper; ASM Press & Snauer
Eukaryotic Cells:
• Plasma membrane: to define its boundary
and retain its content
• Membranous subcompartments
(organelles): various cellular functions
are localized
• Nucleus: to house the DNA
• Cytoplasm:
• Plant cells also have a cell wall outside
the PM
• Animal cells are usually surrounded by an
extracellular matrix.
Membranes in eukaryotic cells
• It consists of phospholipids and
proteins organized into two layers
(Phospholipid bilayer)
• It has a polar (hydrophilic) head and
two nonpolar (hydrophobic) tails.
Diagram of a phospholipid bilayer
From: Life 4th Edition,
by Sinauer Associates
MEMBRANE STRUCTURE AND FUNCTION
5.10 Membranes organize the chemical activities of cells
• Membranes organize the chemical reactions
making up metabolism


Cytoplasm
Figure 5.10
Biological membranes:
• To regulate molecular traffic from one
side to another
• To restrict the passage of materials,
especially polar ones, since its
hydrophobicity of its interior.
• To allow interactions amongst the cells.
(i.e. recognition of WBC).
• To provide energy (mitochondria and
choloroplast)
5.11 Membrane phospholipids form a bilayer
• Phospholipids are
the main structural
components of
membranes
• They each have a
hydrophilic head
and two
hydrophobic tails
Head
Symbol
Tails
Figure 5.11A
• In water, phospholipids form a stable bilayer
– The heads face outward and the tails face inward
Water
Hydrophilic
heads
Hydrophobic
tails
Water
Figure 5.11B
• The plasma membrane of an animal cell
Glycoprotein
Carbohydrate
(of
glycoprotein)
Fibers of the
extracellular
matrix
Glycolipid
Phospholipid
Cholesterol
Microfilaments
of the
cytoskeleton
Figure 5.12
Proteins
CYTOPLASM
Biological membranes:
From http://www.biosci.uga.edu/almanac/bio_103/notes/may_15.html.
Structure of an animal cell
From http://www.biosci.uga.edu/almanac/bio_103/notes/may_15.html.
Nucleus
• Nuclear envelope:
Inner and outer
nuclear membranes
• Nuclear pores
• Nucleolus
From: Life 4th Edition,
by Sinauer Associates
Liver Cell Nucleus
From: www.DennisKunkel.com
Nuclear envelope and
nuclear pores
From: Life 4th Edition,
by Sinauer Associates
From: www.DennisKunkel.com
Nucleus
• Chromatin: DNA associated with proteins, forms
long fibers.
• Each fiber constitutes a chromosome.
• Chromosomes condense during mitosis/meiosis.
• Chromosomes are enclosed within a nuclear
envelope, a double membrane with pores.
• Nucleolus consists of parts of the chromatin
DNA combined with RNA and proteins
(components of ribosomes are made).
Cytoplasm
• Organelles
• cytoskeleton: maintain the shape of
the cell as well as anchoring
organelles, moving the cell and
controlling internal movement of
structures
• Microtubules
• Actin
• Intermediate filaments
Many cell organelles are related through the
endomembrane system
• The endomembrane system is a collection of
membranous organelles
– These organelles manufacture and distribute cell
products
– The endomembrane system divides the cell into
compartments
– Endoplasmic reticulum (ER) is part of the
endomembrane system
Endomembrane System
• Contains
• Rough ER (makes membrane and proteins)
• Smooth ER (makes lipids, destroys toxins, stores
calcium
• Golgi
• Lysosomes
• Vacuoles
• Nuclear envelope
Rough ER
• Contains ribosomes.
• It makes membrane when necessary.
• Some proteins made by RE are inserted into the
ER membrane.
• Phospholipids are made by ER enzymes.
• ER membrane enlarges.
• Makes proteins secreted by the cell.
– Secretory proteins, e.g., antibody, a defensive
molecule. Ribosomes synthesize the proteins of the
antibody, they are assembled in the ER. Short chains
of sugars are linked (glycoprotein), are transported in
the transport vesicle, that buds off.
4.8 Rough endoplasmic reticulum
makes membrane and proteins
• The rough ER manufactures membranes
• Ribosomes on its surface produce proteins
Transport vesicle
buds off
4
Ribosome
Sugar
chain
1
Figure 4.8
Polypeptide
3
Secretory
(glyco-) protein
inside transport
vesicle
Glycoprotein
2
ROUGH ER
Ribosomes
From: Life 4th Edition,
by Sinauer Associates
From: www.DennisKunkel.com
Smooth ER
• Continuous with RE, and lack ribosomes.
• It has enzymes within the membrane.
• Synthesize lipids (fatty acids, phospholipids,
steroids) depending on the type of the cell.
• Regulate the amount of sugar released from liver
cells into the bloodstream.
• Other enzymes break drugs, detoxify.
• SER increase by exposure to drugs and produce
tolerance. Sometimes it can not distinguish
between drugs, so tolerance to a wide range of
drugs occurs. (Barbiturate, a sedative, may
decrease the effectiveness of antibiotics.
4.9 Smooth endoplasmic reticulum
has a variety of functions
• Smooth ER synthesizes lipids
• In some cells, it regulates carbohydrate
metabolism and breaks down toxins and drugs
SMOOTH ER
ROUGH
ER
Nuclear
envelope
Ribosomes
SMOOTH ER
Figure 4.9
ROUGH ER
Endoplasmic Reticulum
From: Life 4th Edition,
by Sinauer Associates
From: www.DennisKunkel.com
4.10 The Golgi apparatus finishes,
sorts, and ships cell products
• The Golgi apparatus consists of stacks of
membranous sacs
– These receive and modify ER products, then send
them on to other organelles or to the cell membrane
Golgi Apparatus
• Flattened sacs looking like a stack of pitabread.
• Sacs are not interconnected.
• A cell may contain a few or a lot of them,
depending on its activity.
• It serves as a molecular warehouse and finishing
factory through modification of substances
manufactured by ER.
Golgi Apparatus
• One side of the Golgi receives the molecule
within the transport vesicle for modification.
• It marks and sorts the molecules into different
batches for different destinations.
• Molecules move from sac to sac in transport
vesicles (they are shipped).
• At the shipping site, they are stored, the finished
products are exported (to membrane, lysosome,
etc.)
Golgi Apparatus
From: Life 4th Edition,
by Sinauer Associates
Golgi Apparatus
From: www.DennisKunkel.com
• The Golgi apparatus
Golgi apparatus
Golgi
apparatus
“Receiving” side of
Golgi apparatus
Transport
vesicle
from ER
New
vesicle
forming
“Shipping”
side of Golgi
apparatus
Transport vesicle
from the Golgi
Figure 4.10
Lysosomes digest the cell’s food and wastes
• Lysosomes are
sacs of digestive
enzymes budded
off the Golgi
LYSOSOME
Nucleus
Figure 4.11A
Lysosomes
• Is produced by the RER and Golgi.
• Lysosome means breakdown body, so they
contain digestive enzymes in a membrane.
• RER puts the enzymes and membranes
together, then Golgi chemically modifies
them, and releases mature lysosomes.
Lysosomes
• Food vacuoles engulf nutrients, lysosomes fuse
with the food vacuoles to digest them. Upon
digestion, amino acids are released and reused.
• Lysosomes destroy harmful bacteria, such that
white blood cells ingest bacteria, later to be
emptied into lysosome.
• Recycling centers for damaged organelles.
Lysosomes
From: Life 4th Edition,
by Sinauer Associates
• Lysosomal enzymes
–
–
–
–
digest food
destroy bacteria
recycle damaged organelles
function in embryonic development in animals
Rough ER
Transport vesicle
(containing inactive
hydrolytic enzymes)
Plasma
membrane
Golgi
apparatus
Engulfment
of particle
Lysosome
engulfing
damaged
organelle
“Food”
LYSOSOMES
Food
vacuole
Figure 4.11B
Digestion
Abnormal lysosomes can cause fatal diseases
• Lysosomal storage diseases are hereditary
– They interfere with other cellular functions
– Examples: Pompe’s disease, Tay-Sachs disease
Lysosomal Diseases
• Lysosomal storage diseases in which a person lacks a
hydrolytic enzyme of the lysosome. Lysosomes
become fat with indigestable substances.
• They are fatal in childhood.
– Pompe’s disease, harmful amounts of glycogen accumulate in
liver cells (lack lysosomal alpha glucosidase).
– Tay-Sachs disease affects the nervous system because
lysosomes lack a lipid digesting enzyme, nerve cells
accumulate excessive lipid molecules.
Vacuoles function in the general maintenance
of the cell
• Plant cells
contain a large
central vacuole
– The vacuole has
lysosomal and
storage functions
Central
vacuole
Nucleus
Figure 4.13A
Vacuoles
• Different types
• Food vacuoles work with lysosomes.
• Plant cells have vacuoles that can serve as a
large lysosome, absorbs water allowing cell to
grow.
• Pigment vacuoles in the petals of a flower.
• Contractile vacuoles, wheels with spikes. Spikes
collect water, and hubs expel it.
• Protists may have contractile vacuoles
– These pump out excess water
Nucleus
Contractile
vacuoles
Figure 4.13B
A review of the endomembrane system
• The various organelles of the endomembrane
system are interconnected structurally and
functionally
Rough
ER
Transport
vesicle
from Golgi
Transport
vesicle
from ER
Plasma
membrane
Vacuole
Nucleus
Lysosome
Smooth
ER
Nuclear
envelope
Golgi
apparatus
Figure 4.14
4.16 Mitochondria harvest chemical
energy from food
• Mitochondria carry out cellular respiration
– This process uses the chemical energy in food to
make ATP for cellular work
Mitochondria
• Mitochondria contain their own DNA
(termed mDNA)
• They function as the sites of energy
release (following glycolysis in the
cytoplasm) and ATP formation (by
chemiosmosis).
• Mitochondria are bounded by two
membranes. The inner membrane folds into
a series of cristae, which are the surfaces
on which ATP is generated.
Mitochondria
From: Life 4th Edition,
by Sinauer Associates
From: www.DennisKunkel.com
Chloroplasts convert solar energy to chemical
energy
• Chloroplasts are found in plants and some
protists
• Chloroplasts convert solar energy to chemical
energy in sugars
Chloroplast
Stroma
Inner and outer
membranes
Granum
Figure 4.15
Intermembrane
space
Chloroplast
• Photosynthesizing organelles of plants and
protists.
• Internal membranes partition the chloroplast into
three major components.
– Intermembrane space between outer and inner
membranes.
– Stroma and network of tubules, and interconnected
hollow discs (grana).
– The space inside the tubules and discs.
Mitochondria
• Convert energy from one chemical form to
another, making ATP.
• Two compartments
– Intermembrane space, a liquid filled compartment.
– In the intermembrane the mitochondrial matrix, in
which cellular respiration takes place.
• Highly folded, enzymes that make ATP are embedded,
folds are called cristae (increase membrane surface area).
MITOCHONDRION
Outer
membrane
Intermembrane
space
Inner
membrane
Cristae
Figure 4.16
Matrix
• When the bond joining a phosphate group to the
rest of an ATP molecule is broken by hydrolysis,
the reaction supplies energy for cellular work
Phosphate
groups
Adenine
Hydrolysis
Energy
Ribose
Adenosine triphosphate
Adenosine diphosphate
(ADP)
Figure 5.4A
Potential energy of molecules
• How ATP powers cellular work
Reactants
Protein
Products
Work
Figure 5.4B
What happens to old, worn-out mitochondria?
Mitochondrial numbers are controlled by autophagy.
This is a process by which lysosomes are involved in
controlling cell constituents. This Figure shows the
process; it is taken from Fawcett, A Textbook of
Histology, Chapman and Hall, 12th edition, 1994.
THE CYTOSKELETON AND
RELATED STRUCTURES
• A network of protein fibers makes up the
cytoskeleton
Figure 4.17A
• Microfilaments of actin enable cells to change
shape and move
• Intermediate filaments reinforce the cell and
anchor certain organelles
• Microtubules
– give the cell rigidity
– provide anchors for organelles
– act as tracks for organelle movement
Microfilaments (e.g., actin)
• provides mechanical strength to the cell
• links transmembrane proteins (e.g., cell surface
receptors) to cytoplasmic proteins
• Used in mitosis
• interact with myosin ("thick") filaments in
skeletal muscle fibers to provide the force of
muscular contraction
Intermediate filaments
• These cytoplasmic fibers average 10 nm in
diameter (and thus are "intermediate" in size
between actin filaments (8 nm) and microtubules
(25 nm).
• Examples:
– keratins are found in epithelial cells and also form
hair and nails;
– nuclear lamins form a meshwork that stabilizes the
inner membrane of the nuclear envelope;
Microtubules
• Microtubules are straight, hollow cylinders have
a diameter of about 25 nm
• are variable in length but can grow 1000 times as
long as they are thick
• are built by the assembly of dimers of alpha
tubulin and beta tubulin.
• are found in both animal and plant cells
Microtubule motors
• There are two major groups of microtubule
motors:
– kinesins
– dyneins
cytoskeleton
From: Life 4th Edition,
by Sinauer Associates
Actin subunit
Tubulin
subunit
Fibrous subunits
25 nm
7 nm
MICROFILAMENT
Figure 4.17B
10 nm
INTERMEDIATE
FILAMENT
MICROTUBULE
Cytoskeleton
• Meshwork of fine fibers for structural support and cell
movement, and transmitting signals.
– Microfilaments: made of actin (globular), a twisted double
chain of actin molecules (change shape).
– Intermediate filaments: fibrous proteins with a ropelike
structure, work for reinforcement and hold tension.
– Microtubules: straight, hollow tubes composed of tubulins,
elongate by adding subunits of tubulin pairs, disassembled.
Cilia and flagella move when
microtubules bend
• Eukaryotic cilia and flagella are locomotor
appendages that protrude from certain cells
• A cilia or flagellum is composed of a core of
microtubules wrapped in an extension of the
plasma membrane
Cilia and Flagella
• Used for locomotion.
• Core of microtubules wrapped in an
extension of the plasma membrane.
• A ring of nine microtubule doublets
surrounds a central pair of microtubules.
• Dynein arms (motors) bends the
microtubules.
FLAGELLUM
Electron micrograph
of sections:
Outer microtubule
doublet
Plasma
membrane
Flagellum
Central
microtubules
Outer microtubule
doublet
Plasma
membrane
Figure 4.18A
Basal body
Basal body
(structurally identical to centriole)
• Clusters of microtubules drive the whipping
action of these organelles
Microtubule doublet
Dynein arm
Figure 4.18B
Sliding
force
EUKARYOTIC CELL SURFACES
AND JUNCTIONS
• Cells interact with their environments and each
other via their surfaces
• Plant cells are supported by rigid cell walls made
largely of cellulose
– They connect by plasmodesmata, channels that allow
them to share water, food, and chemical messages
Walls of two
adjacent
plant cells
Vacuole
PLASMODESMATA
Layers of one
plant cell wall
Cytoplasm
Plasma membrane
Figure 4.19A
• Animal cells are embedded in an extracellular
matrix
– It is a sticky layer of glycoproteins
– It binds cells together in tissues
– It can also have protective and supportive functions
• Tight junctions can bind cells together into
leakproof sheets
• Anchoring
junctions link
animal cells
• Communicating
junctions allow
substances to
flow from cell
to cell
TIGHT
JUNCTION
ANCHORING
JUNCTION
COMMUNICATING
JUNCTION
Plasma
membranes of
adjacent cells
Figure 4.19B
Extracellular
matrix
Epithelial cells
• Epithelia are sheets of cells that provide the
interface between masses of cells and a
cavity or space (a lumen).
• The portion of the cell exposed to the lumen
is called its apical surface.
• The rest of the cell (i.e., its sides and base)
make up the basolateral surface.
Tight Junctions
• They seal epithelial cells
• They prevent the passage
of molecules and ions
through the space
between cells.
• They block the
movement of integral
membrane proteins (red
and green ovals) between
the apical and basolateral
surfaces of the cell.
Human Lung Epithelia
• The epithelial cells of the human lung express a
growth stimulant, called heregulin, on their apical
surface and heregulin receptors, called erbB, on
the basolateral surface.
• As long as the sheet of cells is intact, there is no
stimulation of erbB by heregulin thanks to the seal
provided by tight junctions.
• However, if the sheet of cells becomes broken,
heregulin can reach its receptors. The result is an
autocrine stimulation of mitosis leading to healing
of the wound.
Anchoring (Adherence) junctions
• provide strong mechanical attachments
between adjacent cells.
– They hold cardiac muscle cells tightly together
as the heart expands and contracts.
Adherence junctions
• They are built from:
– cadherins —
transmembrane proteins
(shown in red) whose
extracellular segments
bind to each other and
whose intracellular
segments bind to catenins
(yellow). Catenins are
connected to actin
filaments
Gap Junctions
• are intercellular channels some 1.5 - 2 nm in
diameter. These permit the free passage between
the cells of ions and small molecules (up to a
molecular weight of about 1000 daltons).
• They are constructed from 4 (sometimes 6)
copies of one of a family of a transmembrane
proteins called connexins.
Desmosomes
• Desmosomes are localized
patches that hold two cells
tightly together. They are
common in epithelia (e.g.,
the skin). Desmosomes are
attached to intermediate
filaments of keratin in the
cytoplasm.
4.20 Eukaryotic organelles comprise
four functional categories
• Eukaryotic organelles fall into four functional
groups
Table 4.20
Table 4.20 (continued)