Exploring Life 11/6/2012 12:20:00 PM
Eukaryotic cell: subdivided by internal membranes into various membrane enclosed
organelles. (includes chloroplasts)
Prokaryotic cell: DNA is not separated form the res of the cell by enclosure of a
membrane. (bound nucleus, bacteria and archaea)
Positive feedback: end product speeds up its production. Negative feedback: accumulation of an end product of a process slows that process.
1. Monera a. Prokaryotes
i. Domain Bacteria
ii. Domain Archaea
i. Domain Eukarya **Protists
i. Domain Eukarya
i. Domain Eukarya
i. Domain Eukarya
Describing nature without any preconceived expectations. Hypothesis-Driven Science
Involves constructing a specific testable explanation for a phenomenon based
on a set of observations.
A hypothesis is a testable explanation for an observation.
Inductive reasoning - specific observations to reach a general conclusion.
Deductive reasoning – general observations to reach a specific conclusion.
As we respire we release CO2, the CO2 comes from eating food.
Human proteins can be produced by bacterial cells because all organisms share a
common genetic code.
Darwin could not explain how characteristics are passed from parent to offspring.
-ell: small (organelle) eu: true (eukaryote: true nucleus)
pro: before (prokaryote: no nucleus)
tech: skill or art
biosphere: sum of the plants ecosystems
various kingdoms, groups, domain, etc…
metabolism: the rapid turnover of chemical materials; involves the release or use of
chemical energy. Hormones: biochemical substances produced within plant or animal cells or glands, that
exert a particular effect.
System of nerves and chemical regulators that coordinate activities.
Organisms change their behaviour in response to changes in the surrounding
environment. (active behaviour)
Growth requires an organism to take in material from the environment and organize the
material into its own structure. (living organisms only)
Reproduction: the ability to produce copies.
Asexual reproduction: one parent, cell division.
Sexual reproduction: two parents, both contribute half of the genes.
Evolution: changes that occur within populations and organisms that make individuals
able to adapt to their external environment. (better at response metabolism and
reproduction.) Ecology: the study of relationships between organisms and their relationships with their
Scientific method: orderly process of gaining information about the biological world.
1. State a problem
2. Collect information
3. Form a hypothesis
4. Experiment to test hypothesis
5. Record and analyze data
6. Form a conclusion
Theory: a hypothesis that is confirmed through repeating experimentation. Chemical Basis of Life 11/6/2012 12:20:00 PM
protons and neutrons=mass number
a cloud of negatively charged electrons surround nucleus.
Shell 1=2 electrons
Shell 2=8 electrons
Chemical properties depend mostly on the number of electrons in the outer shell.
Fuller outer shell the more stable an atom is.
Covalent bond: a bond that shares electrons to complete its shell.
Double covalent bond: 2 shared pairs of electrons.
Compound: substance formed by the combination of 2 or more elements.
Electro-negativity: tendency for an atom to pull electrons toward itself.
**atoms do not always share electrons equally. Function of H20 is consequence of its structure.
A molecule with 2 poles – 1 negative and 1 positive = polar molecule
4 properties of H2O
Ability to moderate temperature
The fact that ice floats
Its ability to dissolve substances
H2O = universal solvent
Hydrophobic-H2O fearing (oil, wax, fat, etc…)
**Polar covalent bonds**
acid – increased H+ concentration more acidic lower pH #
base – decreased H+ concentration
more basic lower pH #
1: battery acid
2: digestive juices
3: vinegar, beer, wine
4: tomato juice
5: black coffee
7: pure water (human blood 7.3)
10: milk of magnesia
11: household ammonia
12/13: household bleach
13/14: oven cleaner *the pH of a solution is defined as the negative logarithm of the hydrogen ion
Matter: anything that takes up space or has mass.
Element: a substance that cannot be broken down to other substances by chemical
Compound: a substance consisting of two or more elements combined in a fixed ratio.
*96% of living matter
Trace elements: those required by an organismin only minute quantities.
Atom: the smallest unit matter that still retains the properties of an element. Subatomic particles
o Neutrons, protons, electrons
Neutrons and protons are packed together to form a dense core. (atomic nucleus)
Centre of an ion
For atoms and subatomic particles we use the unit of measurement called a “Dalton”.
Dalton=atomic mass unit
Mass # is approx atomic mass
Some atoms have more neutrons in the same element, these forms are called isotopes. Radioactive isotope: one where the nucleus decays spontaneously, giving off particles
When decay leads to a change in the number of protons, it transforms the atom to an
atom of a different element.
Although radioactive isotopes are useful in biological research and medicine, radiation
Isotopes also poses a hazard to life by damaging cellular molecules.
Only electrons are directly involved in chemical reactions between atoms.
Energy: the capacity to cause change.
Potential: energy: the energy that matter possesses because of its location or structure.
An electron cannot exist in between its fixed states of energy.
Energy levels: different states of potential energy. Electron shell: energy of an electron is correlated with distance from nucleus. This
happens by measurement of “shell” to nucleus.
More energy = farther shell is from nucleus.
**Usually energy when lost is released in the form of heat.
Chemical behaviour of a shell mostly depends on the # of electrons in the outermost
Outermost electrons: valence electrons
Valence shell: outermost shell
Full valence= inert elements (chemically unreactive)
The 3D space where and electron is found 90% of the time is called an orbital.
Each electron shell consists of a specific number or orbitals of distinctive
shapes and orientations.
o 2 electron max per orbital. The reactivity of atoms arises from the presence of unpaired electrons in or more
orbital’s of their valence shells.
When atoms interact to complete their valence shells, it is the unpaired electrons that
Atoms with incomplete valence shell can interact with certain other atoms in such a way,
that each partner completes its valence shell.
Share or transfer
Chemical bonds: the interactions that result in chemical staying close together.
Covalent bond: sharing of a pair of valence electrons by two atoms.
2 or more atoms held together constitutes as a molecule.
Hydrogen (H ) molecular formula H-H structural formula
This forms a single bond.
Oxygen (O ) molecular formula O=O
This forms a double bond. The bonding capacity of an atom generally equal to the number of unpaired electrons in
the atoms outermost shell.
Attraction of a particular kind of atom for the electrons of a covalent bond.
Non-polar covalent bonds: a type of covalent bond in which electrons are shared equally
between two atoms of similar electronegativity.
Polar covalent bonds: a covalent bond between atoms that differ in electronegativity
that shared electrons are pulled closer to the more electronegative atom, making it
slightly negative and the other atom slightly positive.
Example: A charged atom is called and ion.
Because cations and anions are opposite, they attract. This is called an ionic bond.
Compounds formed by ionic bonds are called compounds. (salts)
The attraction between oppositely charged atoms, or ions is an ionic bond. An ionic
bond can form between any two oppositely charged ions, even if they have not been
formed by a transfer of electrons from one to the other.
*The term ion also regards to entire molecules that are electrically charged.
Environment effects the strength of ionic bonds.
A hydrogen bond forms when a hydrogen atom covalently bonded to one
Example: Van Der Waals interactions: weak attractions between molecules or parts of molecules
that are brought about by localized charge fluctuations.
Although weak only when molecules are very close together.
The precise shape of a molecule is usually important to its function in the living cell.
The making and breaking of chemical bonds is called chemical reactions.
The point at which the reactions off set one another exactly is called chemical
Does not mean chemicals are equal in concentration. *An atom is the smallest unit of an element.
Water is the molecule of life, it is a single covalent bond.
Polar molecule: a molecule with opposite charges on opposite sides.
Cohesion: the binding together of like molecules (often hydration).
Adhesion: the attraction between different types of molecules.
Surface tension: a measure of how difficult it is to stretch or break the surface of a liquid.
Kinetic energy: energy of motion. (anything that moves)
Heat: a measure of the total amount of kinetic energy due to molecular motion in the
body of matter.
Temperature: measures the intensity of heat due to the average kinetic energy of
H20: BOIL - 100 FREEZE – 0
HUMANS: 37.6 average Calorie: the amount of heat it takes to raise 1g of H20 by 1 degree
Kilocalorie: the amount of heat it takes to raise 1000g by 1 degree
Joule: 1 joule = .239 cal
Specific heat: the amount of heat that must be absorbed or lost for 1g of that substance
to change its temperature by 1 degree.
Evaporation: liquid to gas.
Heat to vaporization: quantity of heat a liquid must absorb to be converted from a liquid
to a gas.
Evaporative cooling: occurs because the “hottest” molecules, those with the greatest
kinetic energy are lost likely to leave as gas.
Solution: a liquid that is completely homogeneous mixture of two or more substances
called a solution.
Dissolving agent: solvent
Aqueous solution: water is solvent
Ice: hydrogen bonds are stable.
Water: hydrogen bonds reform.
Colloid: a mixture made up of a liquid and particles that remain suspended in that liquid.
Hydrophobic: water fearing Hydrophilic: water loving
Molecular mass: sum of masses of all atoms in the molecules.
Molecular mass = mole
Molarity: # of moles of solute per liter of solution.
Buffers: substances that minimize changes in the H+ and OH- in a solution.
Acid precipitation: rain, snow, fog with a pH lower than 5.6. Molecular Diversity of Life 11/6/2012 12:20:00 PM
Study of carbon compounds is called organic chemistry.
1953: Stanley Miller
concluded organic compounds set the stage for the early origin of life.
Carbon: 6 electrons (4 in valence, 2 in 1 shell)
Shares 4 electrons in outer shell to complete valence shell and become and
(2 tetrahedral groups) o Ethane
Molecule is flat
This tetravalence is one fact of a carbons versatility, that makes large complex molecules
Nitrogen Carbon Urea: CO(NH2)2
Hydrocarbons: organic molecules consisting only of carbon and hydrogen.
Hydrocarbons are the major component of petroleum fossil fuel.
Isomers: compounds that have the same # of atoms of the same elements but difference
in structures mean different properties.
Structural isomers: differs in covalent partners as shown in this example of two isomers
Geometric isomers: differ in arrangement about a double bond in these diagrams, X
represents an atom or group of atoms attached to a double-bonded carbon.
Enantiomers: differ in spatial arrangement around an asymmetric carbon, resulting
molecules that are mirror images. The two isomers are designated L and D isomers. (from the latin left and right, Levo and Dextro.) Enantiomers CANNOT be superimposed
on each other.
Functional groups: components of organic molecules that are most commonly involved
in chemical reactions.
In a hydroxyl group a hydrogen atom bonds with an oxygen atom, which in turn is
bonded to the carbon skeleton of the organic molecule.
Alcohols: name usually ends in “ol”.
Polar as a result of the electronegative oxygen atom drawing electrons toward itself.
Attracts H20 molecules, helping dissolve organic compounds such as sugars.
Example: Ethanol (present in alcoholic beverages) CARBONYL
The carbonyl group consists of a carbon atom joined to an oxygen atom by a double
Ketones: if carbonyl is within a carbon skeleton.
Aldehydes: if carbonyl is at the end of the carbon skeleton.
A ketone and an aldehyde may be structural isomers with different properties, as in the
case for acetone and propanol.
Example: Acetone (Ketone) Propanol (aldehyde) CARBOXYL
When an oxygen atom is double bonded to a carbon atom that is also bonded to a
hydroxyl group, the assembly of atoms is called a carboxyl group (-COOH)
Carboxylic acids: organic acids
Has acidic properties because it is a source of hydrogen ions.
In cells, found in the ionic form, which is called a carboxylate group.
The covalent bond between oxygen and hydrogen is so polar the hydrogen ions tend to
Example: Acetic Acid (gives vinegar a sour taste) AMINO
The amino group consists of a nitrogen atom bonded to two hydrogen atoms and to the
Example: Gylcine (both an amine and carboxylic acid)
Acts as a base, can pick up a proton from a surrounding solution. Ionized with a charge of it under cellular conditions.
Consists of a sulfur atom bonded to a hydrogen atom.
Resembles a hydroxyl group in shape.
Two sulfhydryl groups can interact to help stabilize protein structure.
Example: Ethanethiol PHOSPHATE
In a phosphate a phosphorus atom is bonded to four oxygen atoms, one oxygen is
bonded to the carbon skeleton; two oxygen’s carry negative charges abbreviated P.
The phosphate group ( ) is an ionized form of a phosphate acid group ( )
note that two hydrogens.
Makes the molecule of which it is part an anion. (negatively charged ion)
Can transfer energy between organic molecules.
Example: Glycerol Phosphate: Example: Adenosine Triphosphate
*main energy transferring molecule. Structure of Macromolecules 11/6/2012 12:20:00 PM
100,000+ = macromolecule
polymers (chain like molecules)
(similar, connected by covalent bonds)
monomers: repeating units to serve as building blocks of polymers.
Monomers connected by a reaction where 2 molecules covalently bond through the loss
of an H2O molecule.
Disassembly of polymers to monomers is by hydrolysis (the addition of H2O)
Monosaccharide: have molecular formulas that are some multiple of the unit CH2O. Disaccharide: 2 monosaccharides joined by a glysidic linkage.
Covalent bond between monosaccharides by dehydration synthesis.
Polysaccharides: macromolecules, polymers with a few hundred to thousand
monosaccharides joined by glycosidic linkages.
1-4 linkages (#1 carbon, #4 carbon)
Amylose: most basic, unbranched
Amylopectin: more complex, branched, (#1,#6 linkages)
Wheat, corn, rice: humans diet.
Animals store polysaccharides as glucose.
Chitin o Arthropods
Lipids: fats (hydrophobic)
Constructed from glycerol and fatty acids
Long carbon skeleton
2 fatty acids attached to glycerol, rather than 3. rd
3 hydroxyl group is joined to a phosphate.
**Review Ch. 5 in textbook** Tour of a Cell 11/6/2012 12:20:00 PM
Total surface: height x width x # of sides x # of boxes
Total volume: height x width x # of boxes
Surface to volume ratio: surface area/volume
Flagellum: locomotion organelle present in some animal cells, composed of membrane –
Centrosome: region where the cell’s microtubules are initiated; in an animal cell,
contains a pair of centrioles. Cytoskeleton: reinforces cell’s shape, functions in cell movement, components are
made of protein.
Microvilli: projections that increase the cell’s surface area.
Peroxisome: organelle with various specialized metabolic function; produces hydrogen
Mitochondrion: organelle where cellular respiration occurs and most ATP is generated.
Lysosome: digestive organelle where macromolecules are hydrolyzed.
Golgi Apparatus: organelle active in synthesis, modification, sorting and secretion of a
Ribosome: non membranous organelles that make proteins free in cytoplasm or bound
to rough ER or nuclear envelope.
Plasma Membrane: membrane enclosing the cell.
Nuclear envelope: double membrane enclosing the nucleus; perforated by
pores, contiguous with ER.
Nucleolus: non membranous organelle involved in production of ribsomes; a
nucleus has one or more nucleoli. Chromatin: material consisting of DNA and proteins; visible as individual
chromosomes in a dividing cell.
Endoplasmic reticulum: network of membranous sacs and tubules: other synthetic and
Extracellular Membrane: space between the two cells; sticky and hold cells together.
The nucleus houses the genetic information of the cell – DNA
DNA is wrapped around proteins
2m of DNA per nucleus.
mRNA = messenger RNA
Lysosomes are only found in animal cells.
Centrosome: region where the cell’s microtubules are intitated; lacks centrioles in plant
cells. Golgi Apparatus
Cell wall: outer layer that maintains cell’s shape and protects cell from mechanical
Made of cellulose, proteins and polysaccharides.
Plasmodesmata: channels through cell wall that connect the cytoplasm’s of adjacent
Chloroplasts: photosynthetic organelle, converts energy of sunlight to chemical energy
stored in sugar molecules.
Cytoskeleton: microfilaments, intermediate filaments, microtubules.
Central Vacuole: prominent organelle in older plant cells, functions include storage,
breakdowns of waste products, hydrolysis of macromolecules, enlargement of vacuole is
a major mechanism of plant growth.
Tonoplast: membrane enclosing the central vacuole.
Rough ER Nucleus:
Sugar molecules produced by photosynthesis can be broken down into other molecules
10 = 1,000,000
nucleic acids: information for molecules
deoxyribosenucleic acid (DNA)
ribonucleic acid (RNA)
RNA: intermediary in protein making process DNA’s info is transcribed into RNA which is translated into the primary structure of
DNA is eukaryotic cells – 2 steps
a. Info is transferred from DNA to mRNA
i. RNA leaves nucleus and carries info to the ribosome.
b. The message in the RNA sequence of nucleotides is translated into a sequence
of amino acids. (link and form a polypeptide)
Cell membrane is in constant motion.
Lateral diffusion: membrane; lipids and proteins move sideways in the bilayer.
Lysosome Plasma Membrane
Proteins destined for secretion are made on ribosomes bound to the rough ER.
Move through endomembrane system and are dispatched from Golgi
Apparatus in transport vesicles that moves through cytoplasm and fuses with
Cilia: small, many
Flagella: long, whip like, singular
Use of hydrolysis of ATP to move
Animal cells are connected by junctions
Demosomes (anchoring junctions)
Gap Junctions (communicating junctions)
Plant cells are joined by plasmodemata.
Tight junctions form a barrier between cells preventing fluid from moving between cells. Desmosomes contain keratin
Gap junctions - “bridges”
Plasmodesmata – “bridges” The Working Cell 11/6/2012 12:20:00 PM
We get all our energy and organic molecules from food.
Plasma membrane is selectively permeable.
Does not require energy from the cell
Concentration gradient: moves from where it is more concentrated to less concentrated.
o Does not require energy from the cell
o Diffusion of water across a membrane is called osmosis.
Requires energy from the cell.
Two ions move through a cotransporter protein.
Exocytosis Exportation of materials through vesicles fused with the plasma membrane
and released outside the cell.
The plasma membrane pinches in and forms a vesicle around the material
from the outside of the cell.
Plasma membrane is a fluid mosaic. This means it is diverse with protein molecules
which are embedded in a matrix of phospolipids.
Move fluidly and flexibly
Phospholipids form a two-layer framework called a phospholipid bilayer.
Carbohydrate molecules are attached to some of the molecules that make up
Cells communicate with one another by means of chemical messengers.
The binding of the messenger often triggers a chain reaction involving other
o Called a single transduction pathway The molecules at the end of the pathway perform a certain activity inside the
A transport protein in the plasma membrane forms a channel through which water
molecules or a specific solute can pass.
Hypotonic: lower solute concentration
Hypertonic: higher solute concentration
Phagocytosis(cell eating): the cell engulfs debris, or other object.
Occurs in specialized cells called phagocytes.
Inavgination produces a vacuole which fuses with one o the Lysosomes
containing hydrolytic enzymes.
Materials in the vacuole are then broken down and degraded.
Pinocytosis (cell drinking):the cell engulfs extracellular fluid.
Enter the cell inside a vesicle.
The resulting vesicles travel and release. Receptor-mediated Endocytosis: triggered when receptors bind to external molecules.
Energy is the capacity to do work.
Energy at work: kinetic energy.
Energy in storage: potential energy.
Energy cannot be created nor destroyed.
Energy is lost as heat, cannot be put to use once lost.
The form of energy that drives most of the work in a cell is chemical energy.
Food provides chemical energy when its covalent bonds are broken down.
Input of energy to break down a C-H bond.
A new O-H bond is formed and the extra energy is released.
During cellular respiration, glucose releases energy.
ADP: Adenosine Diphosphate ATP: Adenosine Triphosphate
ATP releases energy when the covalent bond between phosphate groups breaks during
Enzymes do not add energy to a reaction; it speeds up reaction by lowering the energy
An enzyme is very selective.
It only acts on specific molecules
o Called substrate How Cells Harvest Chemical Energy 11/6/2012 12:20:00 PM
In cellular respiration, energy in fuel is converted to ATP.
Most ATP is made in the cell’s mitochondria.
ATP powers the work of the cell.
ATP is produced from a molecule of glucose.
Step one: is called glycolysis.
o Takes place outside of mitochondrion.
o the molecule is split in half.
o NAD+ an electron carrier picks up the electrons and hydrogen atoms
and becomes NADH.
o Pyruvic acid is created.
Step two: pyruvic acid enters the mitochondrion
o One carbon is removed forming a carbon dioxide as a by-product.
o Electrons are stripped, forming NADH.
o Coenzyme A attaches to the 2 carbon fragment which forms acetyl-
Step three: Citric Acid Cycle/Krebs Cycle o Coenzyme A is removed and the remaining 2-carbon skeleton is
attached to an existing 4-carbon molecule that serves as the starting
point for the citric acid cycle.
o The new 6-carbon chain is partially broken down, releasing carbon
o The 6 carbon molecule is split into to molecules of 3 carbons each.
o Several electrons are captured by electron carriers and more carbon
dioxide is released.
o Two ATPs are produced for each molecule of glucose.
Step four: Oxidation Phosphorylation
o Electron carriers deliver their electrons to an electron transfer chain
embedded in the inner membrane of the mitochondrion.
o Electrons are transferred from on carrier to the next.
o As the move along the chain they give up a small bit of energy.
Water is formed as a by-product.
o The energy released by electrons is used to pump hydrogen ions across
the inner membrane of the mitochondrion, creating an area of high
hydrogen ion concentration. o Hydrogen ions flow back across the membrane through a turbine.
o These spinning turbines in the cells produce most of the ATP that is
generated from the food you eat.
10 million ATPs per second in just one cell.
All cells are able to synthesize ATP via the process of glycolysis.
In many cells if oxygen is not present, pyruvate is metabolized in a process called
By oxidizing the NADH produced in glycolysis, fermentation regenerates NAD+, which
can take part in glycolysis to produce more ATP.
The net energy gain in fermentation is 2