Domain 2: Matter

2.1: Organisms must exchange matter with the environment to

grow, reproduce and maintain organization. (EK2.A.3)

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.

Phosphorous and Sulfur:

Phosphorous is found in all nucleic acids. Phosphate groups are used to quickly
store and release free energy in cells. Sulfur is found in all proteins. The major
non-living source of these elements is rocks. Weathering processes release them
in to the soil/water, where they are available for producers to incorporate and
then move through the food chain. Decomposition returns them back to the
environment.

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.

Water molecules occupy most of a cell’s volume.

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Water has major properties that living systems require.

These properties are due to water’s 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.

Temperature buffering: The presence of hydrogen bonds requires more energy to

be absorbed or released by a given amount of water to change the temperature of
that water. This is known as the specific heat of a substance. Water has a very
high specific heat. Water can absorb or release a comparatively large amount of
energy before its temperature changes. Water will keep the environment warmer
when the air cools (because it has a larger store of energy to release), and keep the
environment cooler when the air warms (because it can absorb a larger amount of
energy without changing temperature).
Uses: Insulating the ocean. Keeping living systems within homeostatic
temperature ranges.

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.

The products of the H+ and OH- ion concentrations in an aqueous solution is a

physical constant (10-14). As the concentration of one ion increases, the other
must decrease.

In pure water, the concentrations of H+ and OH- are each 10-7 (one in 10 million).

Acids: substances that increase the amount of H+ ions in an aqueous solution.

This will cause the concentration of OH- ions to decrease.
Bases: Substances that decrease the amount of H+ ions in an aqueous solution.
This will cause the concentration of H+ ions to increase.

pH: a measurement of the concentration of H+ ions in a solution.

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.

Acids have a pH lower than 7. Bases have a pH higher than 7.

Each whole number on the pH represents a power of 10. A solution with a pH

of 5 has a pH that is 100 times more acidic than a solution with a pH of 7.

4. Constraints on Cell Size

Living systems are constrained by the need to exchange matter with the environment.

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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.

Upper limit: Constrained by efficiency.

Surface area: Volume ratio- as a three-dimensonal object’s volume increases, so does

its surface area. However, volume increases as a cubic function of size, while
surface area increases as a squared function.

As volume increases, the efficiency of a cell’s material exchange with the

environment decreases.

Surface Area Increase Adaptations: A variety of structures have evolved to maximize

surface area in cells and increase material exchange efficiency

Examples: root hairs: Plant root cells

Microvilli: Vertebrate intestines

5. MATH Skills: Surface Area:Volume Ratio

Being able to calculate the surface area and volume of an object, if provided with
its physical dimensions.

Use the formula sheet to find relevant equations.

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Sample problem: Determine the relative efficiency of material exchange
for a spherical cell with a radius of 10 µm, and a cubic cell with a side
length of 10µm.

Determine the surface area:volume ratio

Surface Area of cube: 6xarea = 6 x 100um2 = 600um2

Volume of cube: l*w*h = 10 x 10 x 10 = 1000um3

SA:V ratio of cube: 600:1000 = .6

Surface Area of sphere: 4 pi r2 = 4 x 3.14 x 100 = ~1257 um2

Volume of a cube: 4/3 pi r3 = 4/3 * 3.14 * 1000 = ~4189 um3

SA:V ratio of sphere: 1257:4189 = ~.3

Divide the surface area by the volume. Smaller numbers mean more volume per
unit of surface area (less efficiency in transport.

2.2: The subcomponents of biological molecules and their

sequence determine the properties of that molecule.
(EK4.A.1)

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.

All macromolecules are synthesized via condensation reactions (“dehydration

synthesis”- the removal of water) and decomposed via hydrolysis reactions (the
addition of water).

Except for lipids, Macromolecules are polymers, made of repeating subunits

(monomers).

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)

2.3: Variation in molecular units provides cells with a wider

range of functions. (EK4.C.1)

1. Variation in Biological Molecules- Carbohydrates and Lipids

The structure of carbohydrates and lipids determines their function:

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.

2. Variation in Biological Molecules- Proteins

The structure of proteins determines their function:

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.

Secondary structure: Regular 3D structures that arise in polypeptide chains due to

hydrogen bonding between the oxygen, nitrogen, and hydrogen of neighboring
amino acids. Since all polypeptides are made of amino acids, these secondary
structures are found in all proteins.

Tertiary structure: The unique 3D structure (“conformation”) of a particular

polypeptide chain, due to the variety of interactions between the variable groups
of the amino acids in the polypeptide and the influence of the environment that
the polypeptide chain is in.

Quarternary structure: Refers to the overall 3D shape of any protein that is

composed of more than one polypeptide chain. Not all proteins have this level of
structure.

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.

3. Variation in Biological Molecules- Nucleic Acids

Genetic variation leads to molecular variation.

DNA sequence determines protein sequence. Protein sequence contributes to

protein structure. Protein structure determines protein function. Protein
function determines cellular function. Cellular function determines organism
function.

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.

2.4: Cell membranes are selectively permeable due to their

structure. (EK2.B.1)

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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 cell membrane is composed of a phospholipid bilayer with embedded proteins

(the “Fluid mosaic” model). Phospholipid structure causes them to have a
hydrophilic phosphate group “head”, and hydrophobic fatty acid “tails”. This leads
to spontaneous arrangements in water with the phosphate heads pointing toward
the water molecules and the fatty acid tails pointing away. One such arrangement
is the “bi-layer” seen in cell membranes.

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

Cell Wall structure and function:

Many cells have a cell wall external to the cell membrane (animals and animal-like
cells are the only exception). The cell wall is a structure made of structural
polysaccharides (cellulose in plants and plant-like cells) that provides structural
support, but no dynamic control of transport.

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2.5: Growth and dynamic homeostasis are maintained by the
constant movement of molecules across membranes.
(EK2.B.2)

1. Mechanisms of Cellular Transport

Passive Transport:
Refers to the diffusion of material, moving from an area of high concentration to an
area of low concentration across a membrane. No energy is required by the cell to
enable this process.

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.

Endocytosis: Movement of large particles in to the cell.

Exocytosis: Movement of large particles out of the cell.

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).

Three types of tonicity relationships:

Hypertonic: The solution has more solute (and less solvent) than the one being
compared to.

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.

Tonicity relationships and effects on cells:

Without the expenditure of energy, material will always diffuse from high
concentration to low concentration, if it is able to move across the membrane.

Solute will always move from hypertonic solutions to hypotonic solutions.

Solvent will always move from hypotonic solutions to hypertonic solutions. As
long as it is able 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.

Animal-like cells are adapted to exist in isotonic solutions.

Plant-like cells are adapted to exist in hypotonic solutions (the presence of the cell
wall prevents lysis).

3. MATH Skills: Water Potential and Solute Potential

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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 equation:

Ψ – Water Potential
Ψp – pressure potential
Ψs – 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.

Solute potential calculation

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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

Water Potential Solution A = -1.0 * 2M * .0831 * 298K = ~ -49.5 bars

Water Potential Solution B = -2.0 * 1M * .0831 * 290K = ~ -48.2 bars
Water Potential Solution C = -1.0 * 1M * .0831 * 300K = ~ -24.9 bars

Expect C to gain the most water, since water potential is most negative.

2.6: Eukaryotic cells maintain internal membranes that

partition the cell into specialized regions. (EK2.B.3)
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1. Cellular Compartmentalization
Compartmentalization:
Increased compartmentalization allows for increased control of life processes, and
increased efficiency of those processes, as different components of the cell can
function in different environmental conditions.

Different areas of the cell can be specialized to perform different processes.

Eukaryotes vs. Prokaryotes:

The major difference between the organization of eukaryotes and prokaryotes is
the amount of internal compartmentalization.

Prokaryotes: The vast majority of life on earth. Possess no internal

compartments (“organelles”). Unicellular and smaller than eukaryotic cells.

Eukaryotes: Contain many different internal compartments separated from the

rest of the cell by membrane (“organelles”). Most notably, the nucleus, but many
others. Two major types: “plant-like” and “animal-like”, according to how they
process energy. Most eukaryotes are unicellular, too, but all multicellular
organisms (fungi, animals, and plants) are eukaryotes.

Plant-like vs. Animal-like differences:

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.

Golgi Apparatus: A series of flattened membranous disks. Receive vesicles of

membrane and protein from the endoplasmic reticulum and modify those proteins
prior to routing them to their final destinations. Also the site of polysaccharide
production for the cell.

Endoplasmic Reticulum: A series of membranous channels that run throughout the

cell. Responsible for producing all membrane used by the cell and lot of roles in
intercellular transport. Divided in to two parts: smooth and rough
Rough ER: Named because it is covered in “bound” ribosomes. The ribosomes are
producing proteins that will be embedded in membrane or exported from the cell.

Smooth ER: Not covered in ribosomes. Involved in toxin detoxification.

Mitochondria: The site of aerobic cellular respiration. A double-membrane

structure, with a highly-folded inner membrane (a surface area adaptation).

Chloroplasts: The site of photosynthesis. A double-membrane structure with a

highly-folded inner membrane (a surface area adaptation).

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2.7: The structure and function of subcellular components, and
their interactions, provide essential cellular processes.
(EK4.A.2)

1. Organelle structure and function- information processing

Ribosome structure and function:
All cells contain ribosomes. Ribosomes are made of two subunits of RNA and
protein. They are able to assemble and disassemble as required by the cell. In
eukaryotes they are able to associate and disassociate with the endoplasmic
reticulum.

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).

2. Organelle structure and function- matter and energy processing

Mitochondria:
Mitochondria have a double membrane which allows for separation of different
processes that take place in the mitochondria.

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
cell’s 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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