Transcript ecology and evolution

Mr. Lajos Papp
The British International School, Budapest
2013/2014
2. 1 Cell theory
The cell theory states:
1. Living organisms are composed of cells.
2. Cells are the smallest units of life (cells are the basic units
of structure and function in living things).
3. Cells come (arise) from pre-existing cells (by cell
division).
Outline the cell theory.
Exceptions
that
test
the
rule
of
cell
theory:
Muscle cells: challenges the idea that a cell has one
nucleus. Muscle cells have more than one nucleus per
cell. They are surrounded by a single plasma membrane
but they are multi-nucleated (have many nuclei).
Fungal cells: challenges the idea that a cell is a single
unit. Fungal hyphae: very large with many nuclei and a
continuous cytoplasm. The tubular system of hyphae
form dense networks called mycelium. They have cell
walls composed of chitin. The cytoplasm is continuous
along the hyphae with no end cell wall or membrane.
Cells come only from other cells
Cells carry out a form of cell division to form new cells.
This process of cell replication in eukaryotes is called
mitosis and in prokaryotes is called binary fission. The
parental cell divides to produce identical daughter cells.
This aspect of cell theory suggests that all cells
therefore have a common ancestor, the original ancestral
cell form which all other cells have arisen by descent.
This
relationship
of
common
ancestor
therefore that all organisms are related.
suggests
Protoctista: they challenge the idea that a cell is specialised
to a single function. The protoctista cell performs all
functions. Such cells are usually larger than other cells and
are considered as 'acellular', that is, non-cellular.
Discuss the evidence for the cell theory.
Unicellular organisms carry out all the functions of
life including metabolism, response, homeostasis,
growth, reproduction and nutrition.
Compare the relative sizes of molecules, cell membrane
thickness, viruses, bacteria, organelles and cells, using the
appropriate SI unit. Appreciation of relative size is
required (molecules 1 nm, thickness of membranes 10 nm,
viruses 100 nm, bacteria
1 m, organelles up to 10 m,
most cells up to 100 m). The three-dimensional nature /
shape of cells should be emphasised.
If the magnification is X175, it means that 175 cm on
the picture would really be 1 cm.
To calculate magnification:
length on the image / length on the specimen
Scale bar: a scale bar indicates that in reality the length of
the scale bar would measure whatever it says below, e.g. 1
m.
Calculate the linear magnification of drawings and the
actual
size
of
specimens
in
images
of
known
magnification. Magnification could also be stated (for
example, X250) or indicated by means of a scale bar.
Prokaryotic cells are, on average, about 2 micrometers
long. Eukaryotic cells are between 10 and 30
micrometers in diameter. A principal restriction on cell
size is imposed by the relationship between surface
area (SA) and volume (V).
Surface area (SA)
It is through the membrane bound surface of a cell that
materials - such as oxygen, carbon dioxide, ions, food
molecules and waste products - enter and leave the cell.
Volume (V)
These substances are the raw materials and products of
a cell's metabolism, which is the total of all of the
chemical (metabolic) activities in which it is engaged.
The more active the cell's metabolism is, the more
rapidly materials
must
be exchanged
with
the
environment. In smaller cells, the ratio of surface area to
volume (SA/V) is higher than in larger cells.
Thus proportionately greater quantities of materials can
move into, out of, and through smaller cells in a given
period of time. A larger cell, by contrast, requires the
exchange of greater quantities of materials in order to
meet the needs of the larger volume of living matter.
If a cell becomes too large, it cannot absorb oxygen /
CO2 (in plants); cannot absorb foods; cannot excrete
waste products / CO2 fast enough.
Diffusion in the cell becomes slow; centre of the cell is
too far from the membrane; nucleus cannot control a
cell above a certain size; heat is not lost fast enough; not
enough mRNA / proteins / enzymes / ATP produced;
large cells are structurally weak; large blood cells would
not fit through capillaries; sperm cells might not move
quickly enough; having many small cells allows
differentiation.
Summary
As the size of a structure increases, the surface area
to volume ratio decreases.
This is true for organelles, cells, tissues, organs and
organisms.
Explain the importance of the surface area to the
volume ratio as a factor limiting cell size. The rate of
heat
production
/
waste
production
/
resource
consumption of a cell is a function of its volume;
whereas the rate of exchange of materials and energy
(heat) is a function of its surface area.
Simple mathematical models involving cubes and the
changes in the ratio that occur as the sides increase by
one unit could be compared.
Biological organization is hierarchal and shows emergent
properties. With each step upward in the hierarchy of
biological order properties emerge that were not present at
the similar levels (there are properties that cells have that
individual organelles do not; properties that organs have
that the tissues that make them up do not).
These properties result from the interactions between
components. The idea is that the whole is greater than
the sum of its parts.
Multicellular organisms show emergent properties.
Multicellular plants and animals begin their existence as a
single cell. In multicellular organisms, this cell undergoes
a long sequence of changes, which eventually provides all
the different tissues and organs. All cells in an organism
contain identical genetic material.
Yet multicellular organisms consist of a huge range of
specialised cells, for example blood, nerve, muscle and
skin cells. The process that results in these different
specialised cells is called cell differentiation.
Differentiated cells contain the same genetic material as
non-differentiated cells. All human cells contain genes for
the synthesis of the skin pigment melanin. These genes
are on in skin, eye and hair cells. Differentiation involves
no loss or gain of genetic material. When cells
differentiate, some genes are 'switched off' and others are
'switched on'.
The genes necessary for the structure and function of
the cell remain switched on. Other genes are not
expressed; they are switched off.
Once a cell has differentiated, it remains a specialised
cell for its lifetime.
The exact mechanism of cell differentiation has not been
clarified. However, the trigger for the DNA changes during
differentiation seems to be certain chemicals produced in the
immediate environment of the cell.
Explain that cells in multicellular organisms differentiate
to carry out specialized functions by expressing some of
their genes but not others.
Stem cells retain the capacity to divide and have the ability
to differentiate along different pathways.
A stem cell is able to divide but has not yet expressed genes
to specialise to a particular function. Under the right
conditions stem cells can be induced to express particular
genes and differentiate into a particular type of cell. Stem
cells can be obtained from a variety of different places
including the blastocyst.
Blastocyst: a thin-walled hollow structure in early embryonic
development that contains a cluster of cells called the inner
cell mass from which the embryo arises. The outer layer of
cells gives rise to the placenta while the inner cell mass cells
give rise to the tissues of the body. Adults still possess stem
cells in some organs but much less than a child. Even the
placenta can be a useful source of stem cells.
Therapeutic cloning: this is a method of obtaining ES
cells (embryonic stem cells). These stem cells can be used
to treat the individual without generating an immune
response. The human body recognizes and attacks foreign
cells including stem cells. This is a serious barrier to stem
cell therapy.
It begins by taking a somatic (body) cell from the individual.
The somatic cell is fused with an egg that has had its
nucleus removed.
The resulting cell is genetically identical to the individual
because it contains the DNA from the individual’s somatic
cell. The new cell behaves like a fertilized egg and develops
into a blastocyst.
ES cells can be harvested from the blastocyst and grown
in culture. These ES cells could be used to treat the
individual without encountering resistance from his or
her immune system.
1. The patient requires the replacement of some diseased
tissue. First we obtain a health body cell from the
patient.
2. At the same time we require a human egg cell. This is
mainly as the cell retains the tendency to divide.
3. The nucleus is removed from the egg and discarded. The
body cell itself is retained.
4. The nucleus of the patient’s cell is removed and
retained. The body cell is discarded.
5. The nucleus from the patient’s body cell is
transferred to the enucleated egg cell.
6. The cell is then stimulated to divide forming a clone.
7. The cell mass forms a blastocyst.
8. The inner cell mass becomes a source of totipotent stem
cells. Totipotent means they are capable of being
stimulated to become one of any type of cell.
9. Cells are stimulated using differentiation factors to
become the type of cell required for therapy.
10. Therapy would require the transfer of the new healthy
cell to the patient.
Non-Hodgkin lymphoma is a cancerous disease of the
lymphatic system.
1. Patient requires heavy dose of radiation and / or
chemotherapy. This will destroy healthy blood tissue as
well as the diseased tissue.
2. Blood is filtered for the presence of stem cells.
3. Bone marrow can be removed before treatment.
4. Chemotherapy supplies toxic drugs to kill the
cancerous cells.
5. Radiation can be used to kill the cancerous cells but
radiation and chemotherapy are often used together.
6. Post radiation / chemotherapy the patients healthy
blood tissues are also destroyed.
7. Healthy stem cells or marrow cells can be
transplanted back to produce blood cells again.
Outline one therapeutic use of stem cells.
This is an area of rapid development. In 2005, stem
cells were used to restore the insulation tissue of
neurons in laboratory rats, resulting in subsequent
improvements in their mobility.
Any example of the therapeutic use of stem cells in
humans or other animals can be chosen. There are
ethical issues involved in stem cell research, whether
humans or other animals are used.
Use of embryonic stem cells involves the death of
early-stage embryos, but if therapeutic cloning is
successfully developed the suffering of patients with a
wide variety of conditions could be reduced.
Stem cell research has depended on the work of teams
of scientists in many countries, who share results and
so speed up the rate of progress.
However, ethical concerns about the procedures have
led to restrictions on research in some countries.
National governments are influenced by local, cultural
and religious traditions, which vary greatly, and these,
therefore, have an impact on the work of scientists.
2. 2 Prokaryotic cells
The general size of a prokaryotic cell is about 1-2 µm.
1. the absence of membrane bound organelles
2. there is no true nucleus with a nuclear membrane
3. the ribosomes are smaller than in eukaryotic cells
4. the slime capsule is used as a means of attachment to a
surface
5. only flagellate bacteria have a flagellum
6. plasmids are very small circular pieces of DNA that may
be transferred from one bacterium to another.
Draw and label a diagram of the ultrastructure of
Escherichia coli (E. coli) as an example of a prokaryote.
The diagram should show the cell wall, plasma membrane,
cytoplasm, pili, flagella, ribosomes and nucleoid (region
containing naked DNA).
Cytoplasm: contains ribosomes and storage granules
that hold glycogen, lipids; most enzymes needed for
metabolic activities are located here.
Ribosomes: the sites of protein synthesis.
Cell wall: it provides a rigid framework that supports the cell
and maintains its shape. It prevents the cell from swelling and
bursting due to osmosis. Water and small molecules can pass
freely through tiny pores in the wall, but larger molecules like
proteins and nucleic acids are excluded.
Nucleoid: a region containing naked DNA; DNA carries the
genetic material and is the control centre of the cell.
Plasma membrane: it separates the contents of the cells from
their external environments, controlling exchange between the
two and maintaining homeostasis.
Pili: these thread like projections are usually more numerous
than the flagella. In some cases they are involved in the
transfer of DNA in a process called conjugation or
alternatively as a means of preventing phagocytosis.
Flagella: these long thread like attachments are considered
to be for movement. They have an internal protein structure
that allows the flagella to be actively moved as a form of
propulsion.
Annotate (add brief notes to a diagram or graph) the
diagram with the functions of each named structure.
Identify structures in electron micrographs of E. coli.
Prokaryotic cells divide by binary fission. This is an
asexual method of reproduction in which a cell divides
into two same sized cells. The cells are genetically
identical.
Prokaryotic cells divide by binary fission.
2. 3 Eukaryotic cells
DNA
prokaryotes
eukaryotes
circular
linear
naked
associated with
proteins
in cytoplasm
enclosed in a nuclear
envelope
ribosomes
70S
80S
size
0.5 - 5 m
20 m
mitochondria
not present
present
Compare prokaryotic and eukaryotic cells.
Draw and label a diagram of the ultrastructure of a liver
cell as an example of an animal cell. The diagram
should show free ribosomes, rough endoplasmic
reticulum
(rER),
lysosome,
Golgi
apparatus,
mitochondrion and nucleus. The term Golgi apparatus
will be used in place of Golgi body, Golgi complex or
dictyosome.
1:nucleolus; 2:chromatin; 4:nuclear pores; 5:mitochondrion;
6:rough endoplasmic reticulum; 7:ribosomes; 8:Golgi
apparatus; 9:smooth endoplasmic reticulum; 11:lysosomes.
free ribosomes: are important in protein synthesis.
rough endoplasmic reticulum (rER): provides a large
surface area for chemical reactions; provides a pathway for
the transport of materials through the cell; transports
proteins made by ribosomes.
lysosome: it digests material that a cell consumes from the
environment; it digests parts of a cell, such as worn-out
organelles.
Golgi apparatus: produces glycoproteins such as mucin required
in secretions, by adding the carbohydrate part to the protein;
produces secretory enzymes; transports and stores lipids; forms
lysosomes.
mitochondrion: a site for certain stages of cellular
respiration.
nucleus: it contains the genetic material of a cell; acts as a
control centre for the activities of a cell; it is essential for
cell division.
Annotate the diagram with the functions of each named
structure.
http://www.ucmp.berkeley.edu/alllife/ratlivercells.gif
http://faculty.une.edu/com/abell/histo/nuc&cytoEM.jpg
http://faculty.une.edu/com/abell/histo/golgilys.jpg
Identify structures in electron micrographs of liver
cells.
State three differences between plant and animal cells (cell
wall, chloroplasts, carbohydrate storage, vacuole, shape).
Outline two roles of extracellular components. The plant
cell wall maintains cell shape, prevents excessive water
uptake, and holds the whole plant up against the force of
gravity. Animal cells secrete glycoproteins that form the
extracellular matrix. This functions in support, adhesion
and movement.
2.4 Membranes
The fluid mosaic model of the plasma membrane consists of
a phospholipid bilayer with protein molecules found
anywhere between the lipid molecules. In between the lipid
molecules, you find the cholesterol molecules. They keep
the membrane in liquid state.
At low temperature they prevent fatty acids to come too
close to each other; at high temperature they restrict
excessive motion. If a membrane contains a lot of
cholesterol, the membrane will be less fluid (because of the
inflexible ring of cholesterol). The exact composition of the
membrane differs according to the type of membrane (cell
surface, chloroplast, etc.) and the function of the cell.
http://upload.wikimedia.org/wikipedia/commons/e/ee/CellM
embraneDrawing.jpg
Draw and label a diagram to show the structure of
membranes. The diagram should show the phospholipid
bilayer, cholesterol, glycoproteins and integral (embedded
in the phospholipid of the membrane) and peripheral
proteins (attached to its surface). Use the term plasma
membrane not cell surface membrane for the membrane
surrounding the cytoplasm.
A phospholipid contains two fatty acid chains linked to two
of three carbons of a glycerol molecule. The fatty acid
chains make up the nonpolar, hydrophobic portion of the
phospholipid. Bonded to the third carbon of the glycerol is a
negatively charged, hydrophilic phosphate group, which in
turn is linked to a polar, hydrophilic organic group.
Molecules of this type, which have distinct hydrophobic
and
hydrophilic
regions,
are
called
amphipathic
molecules. Because one end of each phospholipid
associates freely with water and the opposite end does not,
the most favourable orientation for them to assume in
water results in the formation of a bilayer structure.
This arrangement allows the hydrophilic head groups of
the phospholipids to be in contact with the aqueous medium,
while the hydrophobic fatty acid chains (tail) are buried in
the interior of the structure away from the water molecules.
Explain how the hydrophobic and hydrophilic properties
of phospholipids help to maintain the structure of cell
membranes.
Protein
channels
allow
communication
between
neighbouring cells by transfer of small molecules (passive
transport).
Transport proteins allow selective passage of essential
molecules, either passively by diffusion or actively by
processes requiring a direct input of energy (sodiumpotassium pump, active transport).
Signal receptor proteins bind external signal molecules and
interact with other membrane proteins that transfer a
message to the cell interior (hormone binding sites).
ATP-driven pumps actively transport ions from one
compartment to another as an energy-storage mechanism.
Immobilized enzymes: enzyme molecules may be
confined within a selectively permeable membrane that
allows a free movement in either direction to the
substrates and products but does not permit the enzyme
molecules to escape.
Cell adhesion: is the binding of a cell to another cell.
Cellular adhesion is regulated by specific adhesion
molecules that interact with molecules on the opposing
surface generally involving protein molecules.
Cell-to-cell communication: proteins in fertilisation,
cell adhesion molecules.
List the functions of membrane proteins including
hormone binding sites, immobilized enzymes, cell
adhesion, cell-to-cell communication, channels for
passive transport (facilitated diffusion) and pumps for
active transport.
The rate of diffusion depends on
charge on the molecule - electric charge prevents
movement.
size - smaller molecules move faster than larger
molecules.
lipid solubility - more highly lipid soluble molecules
move faster.
the
concentration
gradient
-
the
greater
the
concentration difference across the membrane, the faster
the diffusion.
direction relative to the membrane: molecules may
cross the membrane in either direction, depending only
on the direction of the gradient.
Diffusion: the passive movement of particles from a region
of high concentration to a region of low concentration (as
a result of the random motion of particles).
Osmosis: is the passive movement of water molecules,
across a partially permeable membrane, from a region of
lower solute concentration to a region of higher solute
concentration.
Whether a membrane permits a substance to pass through it
depends on the size and charge of its particles and on the
composition of the membrane. A membrane is said to be
permeable to a given substance if it permits it to pass
through, and non-permeable / impermeable if it does not. A
selectively permeable membrane allows some but not other
substances to pass through it readily.
In general, biological membranes are most permeable to
small molecules and to lipid-soluble substances able to cross
the hydrophobic interior of the layer. Although they are
polar, water molecules can rapidly cross a fluid lipid bilayer
because they are small enough to pass through gaps that
occur as a fatty acid chain momentarily moves out of the
way.
Gases such as oxygen, carbon dioxide; and small polar
molecules like glycerol; plus larger, non-polar substances such
as hydrocarbons can also freely traverse (cross) a lipid bilayer.
Slightly larger polar molecules, such as glucose, and charged
ions of any size do not pass freely through the lipid bilayer,
either because of their size or because they are repelled by a
layer of electrical charges on the surface of the membrane.
Although the lipid bilayer is relatively impermeable to
ions, cells must be able to move ions and polar
molecules across membranes. The permeability of
membrane to those substances is due to the activities of
membrane proteins.
Facilitated
diffusion:
channel
proteins
(show
specificity for the structure of the transported substance)
help molecules cross the bilayer. Movement is down the
concentration gradient, faster than simple diffusion, no
energy is required, ions: (Na+, K+, Cl-) and glucose.
Explain passive transport across membranes by simple
diffusion and facilitated diffusion.
Active transport: although adequate amounts of some
substances can be transported across cell membranes by
diffusion, a cell often needs to move solutes against a
concentration gradient. Many substances are required by the
cell in concentrations higher than those outside the cell.
Active transport requires that particles be pumped from a
region of low concentration to a region of high
concentration (that is against concentration gradient), the
energy inherent (built-in) in the gradient is unavailable and
hence a different energy source (ATP provides energy by
hydrolysing to ADP) is required.
Protein pumps are involved in active transport. Each
pump only transports particular substances, so cells can
control what is absorbed and what is expelled.
Carrier-assisted transport: can move substances against a
concentration
gradient,
energy
is
required,
sodium-
potassium pump; some algae pump iodine inwards to reach
a 2x106 higher concentration inside.
Explain the role of protein pumps and ATP in active
transport across membranes.
http://www.youtube.com/watch?v=kfy92hdaAH0
Proteins are synthesised by ribosomes and then enter the
rough endoplasmic reticulum. Vesicles bud off from the rER
and carry the proteins to the Golgi apparatus. The Golgi
apparatus modifies the proteins. Vesicles bud off from the
Golgi apparatus and carry the modified proteins to the
plasma membrane.
Summary
1. Protein is already synthesised and present in the rER.
2. The protein is moved through the rER and modified.
3. A spherical vesicle is formed form the end of the rER with the
protein inside.
4. The vesicle migrates to the Golgi apparatus.
5. Vesicle and Golgi membranes fuse. The protein is released into
the lumen of the Golgi apparatus.
6. The Golgi modifies the protein further.
7. A new vesicle is formed from Golgi membrane that then breaks
away.
8. The vesicle migrates to the plasma membrane → fuses →
secretes its content. This process is called exocytosis.
Explain how vesicles are used to transport materials within a
cell between the rough endoplasmic reticulum, Golgi apparatus
and plasma membrane.
Membranes are not static structures. The molecules
making up the membrane can move in the plane of the
membrane. Small amounts of membrane can be added
or removed without tearing the membrane (endo- and
exocytosis).
Endocytosis:
1. part of the plasma membrane is pulled inwards;
2. a droplet of fluid becomes enclosed when a vesicle is
pinched off;
3. vesicles can then move through the cytoplasm
carrying their contents.
Exocytosis:
vesicles fuse with the plasma membrane;
the contents of the vesicle are expelled;
the membrane then flattens out again.
http://highered.mcgraw-hill.com/olc/dl/120068/bio02.swf
Describe how the fluidity of the membrane allows it to change
shape, break and reform during endocytosis and exocytosis.
2.5 Cell division
The cell cycle describes the major phases of activity between cell
division of a cell. The length of the cell cycle depends on the
particular cell. For example, bacterial cells can divide every 20
minutes under suitable conditions, skin cells divide about every
12 hours on average, liver cells every two years, and muscle cells
never divide at all after maturing, so remain in the growth phase
for decades. The total length of a cell cycle varies depending on
the specialised function of a cell.
Interphase: the longest phase which itself occurs in
three stages
G1: the cell performs its normal differentiated function.
Protein
synthesis
/
chloroplast replication
mitochondrion
replication
/
S: DNA replication. At this point the mass of DNA in the
cell has doubled
G2: preparation for cell division
Mitosis: phases
Cytokinesis: division of the cytoplasm to form two
daughter cells.
Outline the stages in the cell cycle, including
interphase (G1, S, G2), mitosis and cytokinesis.
Tumours (cancers) are the result of uncontrolled cell
division and that these can occur in any organ or
tissue.
Interphase is an active period in the life of a cell when
many metabolic reactions occur, including protein
synthesis, DNA replication and an increase in the
number of mitochondria and / or chloroplasts.
Prophase: chromosomes become visible (supercoiling);
centrioles move to opposite poles (splitting); spindle
microtubules formation; nucleolus becomes invisible;
nuclear membrane disappears.
Metaphase: chromosomes move to the equator;
centromeres attach to spindle microtubules (extending
from each pole to the equator).
Anaphase: sister chromatids separate and move to
opposite poles as individual chromosomes.
Telophase: chromosomes have reached the poles;
spindle disappears; centrioles replicate (in animal cells);
nuclear membrane reappears (reformation); nucleolus
becomes visible; chromosomes become chromatin and
no longer visible.
Describe the events that occur in the four phases of mitosis
(prophase, metaphase, anaphase and telophase). Include
supercoiling
of
chromosomes,
attachment
of
spindle
microtubules, splitting of centromeres, movement of sister
chromosomes
to
opposite
poles
and
breakage
and
reformation of nuclear membranes. Textbooks vary in the
use of the terms chromosome and chromatid.
In this course, the two DNA molecules formed by DNA
replication are considered to be sister chromatids until
the splitting of the centromere at the start of anaphase;
after this they are individual chromosomes.
Explain how mitosis produces two genetically identical
nuclei.
The significance of mitosis is its ability to produce daughter cells
that are exact copies of the parental cell. It is important in four
ways:
1. growth - if a tissue is to extend by growth, it is important that
the new cells are identical to the existing cells.
2. embryonic development - mitosis produces an increasing
number of smaller cells, each with an exact copy of the genome
present in the zygote; cleavage: it refers to the early cell divisions
that occur as a fertilized egg begins to develop into an embryo.
3. tissue repair - damaged cells must be replaced by exact copies
of the originals if the repair is to return a tissue to its former
condition.
4. asexual reproduction - if a species is successful in colonising
a particular habitat, there is little advantage, in the short term, in
producing offspring that differ from the parents, because these
may be less successful. It is better to quickly establish a colony of
individuals that are similar to the parents.
Growth, embryonic development, tissue repair and asexual
reproduction involve mitosis.