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1. Matter exchange
The atoms in living systems are common on this planet. Living systems are mostly
made of 6 elements
and a handful of other trace elements.
Living systems cycle matter from the environment, turning it in to biologically useful
molecules before
returning it back to the environment through life processes.
Carbon:
Carbon is the major structural atom in all organic molecules. The major non-
living source of carbon is the atmosphere (as CO2). Carbon is incorporated in to
producers through photosynthesis and from there in to living systems through the
food chain, and returned back to the environment through cellular respiration,
and decomposition.
Oxygen:
Oxygen is also found in most organic molecules. The major non-living source of
oxygen is the atmosphere (as O2) and water (also the major non-living source of
hydrogen). Oxygen is incorporated in to cellular respiration and through the food
chain. Oxygen is returned back to the environment through photosynthesis.
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Nitrogen:
Nitrogen is found in all proteins and nucleic acids (present in all living systems).
The major non-living source of Nitrogen is the atmosphere (as N2). Nitrogen is
incorporated in to the food chain through the action of nitrogen-fixing bacteria,
which convert N2 in to molecules that can be used by producers (NO3-), and from
producers through the food chain. Nitrogen is returned back to the environment
through decomposition and the action of denitrifying bacteria.
Hydrogen:
Hydrogen is a major component of all organic molecules. It is the most common
atom in the Universe. It enters biological systems largely bonded to oxygen in
water, and is returned to the environment by decomposition and water release.
2. Properties of Water
Water is a major component of all living systems.
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Water has major properties that living systems require.
These properties are due to waters polarity (unequal sharing of electrons, leading to
a partially positive
and partially negative charge).
Hydrogen Bonds: the polarity of water results in attractive forces between the
oxygen and hydrogen atoms of neighboring water molecules. This makes water
cohesive (attracted to itself) and adhesive (attractive to anything else that has
positive or negative charges).
Uses: Transpiration pull, dissolving of substances.
3. MATH Skills: pH
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Water dissociates. A water molecule can be pulled apart into a proton (H+) and a
Hydroxide ion (OH-) by other water molecules. This happens ~ once for every
10,000,000 (107) water molecules.
In pure water, the concentrations of H+ and OH- are each 10-7 (one in 10 million).
pH = - log [H+]
This is a complicated way of saying that we can take the exponent of the pH
concentration and negate it (make it positive) to state the pH.
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Cellular life has an upper and lower limit on the size a cell can be:
Lower limit: Constrained by the need to have a certain amount of matter inside
the cell in order to keep functioning.
Being able to calculate the surface area and volume of an object, if provided with
its physical dimensions.
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Sample problem: Determine the relative efficiency of material exchange
for a spherical cell with a radius of 10 m, and a cubic cell with a side
length of 10m.
Divide the surface area by the volume. Smaller numbers mean more volume per
unit of surface area (less efficiency in transport.
1. Biological Molecules
Living systems are made of four major types of Macromolecule:
Carbohydrates- Sugars: function in short-term energy storage and structural
support.
Lipids- Fats, oils, waxes: function in long-term energy storage, cell membrane
structure, and cell signaling.
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Proteins- function in all cellular processes.
Nucleic Acids- DNA and RNA: function in information storage and expression of
that information by determining protein sequences.
Carbohydrates:
Monomer: Monosaccharide \ Polymer: polysaccharide
Monosaccharides exist as ring structures.
Lipids:
Steroids, triglycerides, and phospholipids.
Proteins:
Monomer: Amino acid \ Polymer: polypeptide
There are 20 different types of amino acids used in biological systems. They all have
the same Backbone structure, but differ based on the composition of the
variable group that is bonded to the central carbon.
The bond between two amino acids is referred to as a peptide bond.
Nucleic Acids:
Monomer: nucleotides \ Polymer: nucleic acid
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There are two types of nucleic acids in biological systems (DNA and RNA). Each one
is made of four types of nucleotides, which differ from each other based on the
type of nitrogenous base that they contain (DNA: ACTG / RNA: ACUG)
Ex: Cellulose vs. Amylose (starch): Both are polysaccharide polymers of glucose
monomers, but they vary in the connections between monomers. As a result,
cellulose is not easily digested, while amylose is very easily digested.
Ex: Lipid membrane composition: Cells will vary the lipid composition of their
membranes in order to respond to changes in temperature. One example-
changes in cholesterol concentration to resist increasing and decreasing
membrane fluidity.
Proteins are functionally responsible for all cellular processes. They have a wide and
diverse variety of functions, which are determined by their structure. Protein
structure is discussed at four levels of organization:
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Primary structure: the sequence of amino acids in a polypeptide. This is
determined by DNA. Each amino acid is joined to the next via a peptide bond.
Ex: Adult hemoglobin vs. fetal hemoglobin: Differences in the polypeptide chains
that comprise fetal hemoglobin give the molecule a higher binding affinity to
oxygen, which is necessary since the fetus needs to get its oxygen from its mothers
hemoglobin.
Ex: Antibody structure: Differences in the variable regions of the proteins that
comprise antibodies makes it possible to create millions of different possible
antibodies.
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Denaturation: The disruption of the structure of a macromolecule leading to a
disruption of its function. Caused by changes to the environment of the molecule.
A change in DNA sequence can affect all levels of function in a living system.
Ex: Sickle cell anemia- one nucleotide change leads to one amino acid change. This
change alters the function of hemoglobin, and leads to major disease effects in the
organism.
New functions can arise via genetic duplications. The duplication of genetic
information allows for new variations and adaptations.
Ex. Antifreeze gene in fish- allows fish to live in freezing temperatures. Evolved
from pre-existing genes.
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1. Cell Membrane Structure
Cell membrane structure and function:
The cell membrane is the boundary between the cell and the environment. It also
allows the cell to control which substances pass in to and out of the cell.
The membrane proteins have a variety of functions: transport, cell-cell contact and
recognition, anchorage, enzymatic functions, and others.
Selective Permeability:
Selective permeability is controlled through control of the proteins present in the cell
membrane. Only small, non-polar molecules are able to move through the
phospholipid bi-layer. All other substances must move through proteins
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2.5: Growth and dynamic homeostasis are maintained by the
constant movement of molecules across membranes.
(EK2.B.2)
Simple/Facilitated Diffusion:
Simple diffusion: movement through the bi-layer. Only small non-polar molecules
can do this.
Facilitated diffusion: movement through a protein channel. Any molecule that is not
small and nonpolar must diffuse through a protein pore in the membrane.
Ex: aquaporins.
Active Transport:
Refers to the movement of material from an area of low concentration to an area of
high concentration.
This requires energy, in order to work against the natural tendency for molecules to
diffuse. Cells always use
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Ex: Na/K pump: In order to move sodium out of the cell and potassium in to the
cell to establish specific concentrations. ATP is used to provide the energy needed
to modulate the shape of the pump proteins.
Bulk Transport:
The movement of large molecules in to or out of the cell. Requires the use of a
vesicle.
2. Analyzing Transport
Tonicity:
A measurement of the relative concentrations of solute and solvent in two
different solutions.
Used to be able to determine how a cell (its internal solution) will respond when
placed in to different aqueous environments (the external solution).
Hypotonic: The solution has less solute (and more solvent) than the one being
compared to.
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Isotonic: The solution has the same amount of solute (and solvent) as the one
being compared to.
Cells placed in hypertonic solutions will gain solute and lose solvent (water).
Plasmolysis: The loss of water
Cells placed in hypotonic solutions will lose solute and gain solvent (water).
Lysis: The bursting of the cell membrane.
Plant-like cells are adapted to exist in hypotonic solutions (the presence of the cell
wall prevents lysis).
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Water Potential: A measurement of how likely water is to diffuse (osmosis) in to
an area.
Water will move from areas of higher water potential to areas of lower water
potential. Pure water is assigned a water potential of 0 (no net diffusion)
Water potential depends on several different factors, but we only focus on the
pressure difference (the pressure potential) and the tonicity (the solute
potential) as they are the only significant factors in biological systems.
Water Potential
p pressure potential
s solute potential
The typical units of water potential are bars aka torr aka mmHg in a barometer.
In any open air system with no active pressure generation, the pressure potential will
be zero, and the water potential will depend entirely upon the solute potential.
This is the typical case when investigating diffusion and osmosis in the lab.
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i = ionization constant for the solute (1.0 for sucrose, 2.0 for NaCl, etc.)
C = molar concentration of the solute
R= pressure constant 0.0831 liter bars/mole K
T= temperature in Kelvin (C + 273)
Sample Problem:
Determine which of the following solutions will gain the most water if placed in
to a sample of pure water in a piece of dialysis tubing at the temperature
indicated. Assume all samples are at atmospheric pressure:
Solution: Solute: Tonicity: Temperature
A Sucrose 2M 298K
B NaCl 1M 290K
C Glucose 1M 300K
Expect C to gain the most water, since water potential is most negative.
Plant-like cells contain chloroplasts (for photosynthesis), a large central vacuole, and
an external cell
wall. Animals do not have any of these organelles.
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2. Major Eukaryotic Organelles
Major Eukaryotic Organelles:
Nuclear membrane: Surrounds and separates the DNA from the rest of the cell.
Contains pores to allow material to enter and exit the nucleus and interact with
the DNA.
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2.7: The structure and function of subcellular components, and
their interactions, provide essential cellular processes.
(EK4.A.2)
Endomembrane System:
The cellular system by which the information in DNA is expressed and
incorporated in to cellular processes:
Nucleus ! ER ! Golgi ! final destination (membrane or export).
The highly folded inner membrane (the cristae) contains many copies of the
enzymes needed to produce ATP by the cell, with maximized surface area.
Chloroplasts:
Chloroplasts have a double outer membrane with inner membranous stacks called
thylakoids.
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The membrane of the thylakoid contains many copies of the enzymes and
chlorophyll needed to produce chemical energy from solar radiation during the
first part of photosynthesis (the light reactions).
The inside of the thylakoids (the stroma) contain the enzymes needed to produce
chemical compounds during the second part of photosynthesis (Carbon fixation).
Lysosomes:
Lysosomes are membrane-enclosed sacs that contain collections of digestive,
hydrolytic enzymes. Lysosomes serve roles in digestion of molecules, recycling a
cells damaged components, and programmed cell death.
Vacuoles:
A vacuole is a membrane-bound sac that stores material. Plants have a large
central vacuole that increases the cells surface area: volume ratio by decreasing the
active volume of the cell.
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