Life Science summary: Chapters 1 to 5

Chapter 1
Paragraph 1.1
What is biology?
Biology is the scientific study of living things (organisms).
Characteristics living organisms:
Made of a common set of chemical components
Their building blocks are cells
Their cells convert molecules into new biological molecules
Their cells extract energy from the environment and use it for biological work
They contain genetic information that uses a code to specify the assembly of proteins
They replicate genetic information when they reproduce
They self regulate their internal environment
Life arose from non-life via chemical evolution:
Complex biological molecules first arose through the random physical association of
chemicals in that environment
Critical step evolution of life appearance nucleic acids
Nucleic acids molecules that can reproduce themselves and serve as templates for the
synthesis of proteins
Cellular structure evolved in the common ancestors of life:
Another important step the enclosure of complex proteins and other biological molecules
by membranes that contained them in a compact internal environment separate from the
external environment
Fatty acids played critical role because they don't dissolve in water, but form membranous
films which can form spherical structure
Prokaryotes unicellular and enclose by a single outer membrane
Two main groups of prokaryotes bacteria and archaea
Eukaryotes have outer and inner membranes that enclose specialized organelles within
their cells
Cellular specialization enabled multi-cellular eukaryotes to increase in size and become
efficient at gathering resources and adapting to specific environments
Photosynthesis allows some organisms to capture energy from the sun:
Prokaryotes took small molecules form their environment and broke them down to their
component atoms releasing and using the energy contained in the chemical bonds
Aerobic metabolism biochemical process that uses 0 to extract energy from nutrient
molecules
Anaerobic metabolism does not use 0
Biological information is contained in a genetic language common to all organisms:
Genome the sum total of all the DNA molecules contained in each cell
Genes specific segments of DNA that encode the information the cell uses to create amino
acids and form them into proteins
Protein molecules govern chemical reactions within cells and form much of an organism's
structure
Populations of all living organisms evolve:
Population group of individuals of the same species that interact with one another
Evolution the change in the genetic makeup of biological populations throughout time
Adaptations structural, physiological, or behavioral traits that enhance an organism's
chance of survival and reproduction in its environment
Biologists can trace the evolutionary tree of life:
Phylogenetic trees that portray the evolutionary histories of the different groups of
organisms
Cellular specialization and differentiation underlie multi-cellular life:
Tissues assemblage of differentiated cells
Organs organized different tissue types
Organ systems organs whose functions are interrelated
Living organisms interact with one another:
Community populations of all the species that live and interact in a defined area
Ecosystem communities together with their environment
Nutrients supply energy:
Nutrients supply the organism with energy and raw materials for carrying out biochemical
reactions
Basis cellular work is building/synthesis of new complex molecules and structures from
smaller chemical units
The myriad biochemical reactions that take place in cells are integrally linked in that the
products of one reaction are the raw materials of the next
Living organisms must regulate their internal environment:
Internal environment: its physical and chemical composition must be maintained within a
narrow range of physiological conditions that support survival and function
Homeostasis maintaining this narrow range
Paragraph 1.2
Scientific methods combine observation, experimentation, and logic:
Inductive logic involves taking observations or facts and creating a new proposition that is
compatible with those observations or facts.
Deductive logic starts with a statement(hypothesis) believed to be true and then goes on
to predict what facts would also have to be true to be compatible with that statement
Hypothesis-prediction approach:
1. Making observations
2. Asking questions
3. Forming hypothesis, which are tentative answers to the questions
4. Making predictions based on the hypotheses
5. Testing predictions by making additional observations or conducting experiments
Good experiments have the potential to falsify hypotheses:
The most informative experiments are those that have the ability to show that the prediction
is wrong then the hypothesis can be questioned, modified or rejected
Controlled experiment manipulates one or more of the factors being tested
Comparative experiments compare un-manipulated data gathered from different sources
Independent variable variable that is manipulated
Dependent variable response that is measured
Nine levels of biological organization:
1. molecules
2.cell
3.tissue
4.Organ
5.Organisms
6.Populations
7.Community
8.Ecosystem
9.Bioshpere

Chapter 2
Paragraph 2.2 how does atomic structure explain the properties of matter?
An element consists of only one kind of atom:
Element pure substance that contains only one kind of atom
98% of the mass of every living organism is composed out of six elements: Carbon(C),
Oxygen(O), Hydrogen(H), Phosphorus(P), Nitrogen(N), Sulfur(S)
Each element has a unique number of protons:
Atomic number the number of protons
Mass number of an atom total number of protons and neutrons in its nucleus
The number of neutrons differs among isotopes:
Isotopes have the same number of protons but a different amount of neutrons
Isotopes are formed when atoms combine and/or release particles
Atomic weight equivalent to the average of the mass numbers of a representative sample
of atoms of that element, with all the isotopes in their normally occurring proportions
The behavior of electrons determines chemical bonding and geometry:
The behavior of electrons explains how chemical reactions occur
Orbital region where the electron is most likely to be
Electron shells:
First shell consists of one orbital, max electrons is 2
Second shell contains four orbitals, can hold up to 8 electrons
Additional shells can hold up to 8 electrons, the farther a shell is form the nucleus, the
higher the energy level is for an electron occupying that shell
Paragraph 2.2 how do atoms bond to form molecules?
Chemical bond attractive force that links two atoms together in a molecule
Covalent bonds consist of a shared pairs of electrons:
Covalent bond forms when two atoms attain stable electron numbers in their outermost
shells by sharing one or more pairs of electrons
Compound pure substance made up of two or more different elements bonded together
in a fixed ratio
Orientation:
For a given atom within a molecule, the angle of each of its covalent bonds, with respect to
the other bonds, is generally the same
Even though the orientations of bonds around each atom are fairly stable, the shapes of
molecules can change
Multiple covalent bonds:
Two atoms can share more than one pair of electrons
Single bond sharing a single pair of electrons
Double bond sharing two pairs of electrons
Triple bond sharing three pairs of electrons
Unequal sharing of electrons:
Electro-negativity the attractive force that an atomic nucleus exerts on electrons in a
covalent bond
Non-polar covalent bond two atoms who are close to each other in electro-negativity and
will share electrons equally
Polar covalent bond when electrons are drawn to one nucleus more than to the other
Polar bond is called polar because the opposite charges are separated at the two ends, or
poles, of the bond

Ionic attractions form by electrical attraction:

Ion electrically charged particles that form when atoms gain or lose one or more electrons
Complex ions groups of covalently bonded atoms that carry an electric charge
Ionic attractions bonds are formed as a result of the electrical attraction between ions
bearing opposite charges
Ions can form bonds that result in stable solid compounds, which are referred to by the
general term salts
Under conditions in livings cells is an ionic attraction less strong than a non-polar covalent
bond
Hydrogen bonds may form within or between molecules with polar covalent bonds:
Hydrogen bond the bond hydrogen(negatively charged) atoms form when they encounter
a negatively charged oxygen atom
Hydrogen bonds are NOT restricted to water molecules
A hydrogen bond is weaker than most ionic attractions because its formation is due to partial
charges
Hydrophobic interactions bring together non-polar molecules:
Polar molecules can interact with each other through the weak attraction of hydrogen bonds
this is called hydrophilic(water loving)
Hydrocarbon molecules molecules containing only hydrogen and carbon atoms, they are
non-polar
In water these molecules tend to aggregate with one another rather than with the polar
water molecules non-polar molecules are known as hydrophobic(water hating)
Van der Waals forces involve contacts between atoms:
The interaction between non-polar substances are enhanced by van der Waals forces
which occur when the atoms of two molecules are in close proximity
Although a single van der Waals interaction is brief and weak, the sum of such interactions
over the entire span of a large non-polar molecule can result substantial attraction

Paragraph 2.3 how do atoms change partners in chemical reactions?

A chemical reaction occurs when moving atoms collide with sufficient energy to combine or
to change their bonding partners
In a oxidation-reduction reaction electrons and protons are transferred
Energy the capacity to do work, or in chemical terms the capacity for change

Paragraph 2.4 what makes water so important for life?

Water has a unique structure and special properties:
The water molecule has a tetrahedral shape and it is polar
Ice floats:
Solid water is less dense than liquid water this is why ice floats
Ice requires a great deal of heat energy to melt because a lot of hydrogen bonds must be
broken in order for water to change from solid to liquid
Specific heat the amount of heat energy required to raise the temperature of 1 gram the
substance by 1C
Heat of vaporization the amount of heat that is required to change a substance from it's
liquid to its gaseous state
Cohesion and surface tension:
Cohesion the capacity of water molecules to resist coming apart from one another when
placed under tension

The reactions of life take place in aqueous solutions:

Qualitative analysis deal with the identification of substances involved in chemical reactions
Quantitative analysis measure concentrations or amounts of substances
Avogadro's number 6.02 x 10
Aqueous solutions may be acidic or basic:
Acids substances that release H
Bases substances that accept H
The ionization of strong acids and bases in water is virtually irreversible
The ionization of weak acids and bases in water is somewhat reversible
A lower pH means a higher H concentration, or greater acidity
Buffers:
Buffer solution that maintain a relatively constant pH even when substantial amounts of
acid or base are added
Buffer is a mixture of a weak acid and its corresponding base, or a weak base and its
corresponding acid
Chapter 3
Paragraph 3.1
What kinds of molecules characterize living things:
Proteins are formed from different combinations of 20 amino acids
Carbohydrates can form giant molecules by linking together chemically similar sugar
monomers to form polysaccharides
Nucleic acid are formed form four kinds of nucleotide monomers linked together in long
chains
Lipids form large structures form a limited set of smaller molecules, but in this case non-
covalent forces maintain the interaction between the lipid monomers
Macromolecules polymers with molecular weights exceeding 1,000

Functional groups give specific properties to biological molecules:

Functional group certain small groups of atoms, with specific chemical properties
They can confer those properties to larger molecules
Macromolecules contain many different functional groups, for example a polar, hydrophobic
and charged functional group
These functional groups help determine the shape of the macromolecule and how it interacts
with other molecules
7 functional groups and their properties:
Hydroxyl polar, hydrogen bonds with water to help dissolve molecules. Enables linkage to
other molecules by condensation
Aldehyde C=O group is very reactive. Important building molecule and in energy-releasing
reactions
Keto C=O group is important in carbohydrates and in energy reactions
Carboxyl acidic. Some carboxylic acids important in energy releasing reactions.
Amino basic.
Phosphate acidic. When bonded to another phosphate, hydrolysis releases much energy
Sulfhydryl by giving up H two -SH groups can react to form a disulfide bridge, thus
stabilizing protein structure
Isomers have different arrangements of the same atoms:
Structural isomers differ in how their atoms are joined together
Cis-trans isomers involve a double bond between two carbon atoms, where the carbons
share two pairs of electrons
Optical isomers occur when a carbon has four different atoms or groups of atoms attached
to it
The structures of macromolecules reflect their functions:
Each type of macromolecule performs one or more functions such as energy storage,
structural support, catalysis, transport of other molecules, regulation of other molecules,
defense, movement or information storage
What they do depends on their shape
Most macromolecules are formed by condensation and broken down by hydrolysis:
Condensation reaction polymers are formed, loss of water
Hydrolysis reaction polymers are broken down, water is made
Paragraph 3.2 what are the chemical structures and functions of proteins
Amino acids are the building blocks of proteins:
Amino acid has a carboxyl functional group and a amino functional group
The 20 amino acids found in living organisms are grouped and distinguished by their side chains:
Five amino acids have electrically charged(ionized) side chains, they attract water
Five amino acids have polar side chains, they are hydrophilic
 Seven amino acids have non-polar side chains and are hydrophobic
Three special amino acids:
Cysteine has a SH group can react with another cysteine side chain in an oxidation reaction
called a disulfide bridge
Glycine consists of a singel hydrogen atom
Proline forms a covalent bond with the hydro-carbon side chain, resulting in a ring
structure
Peptide linkages form the backbone of a protein:
In the C-N linkage the adjacent carbons are not free to rotate fully
The oxygen bound to the carbon in the carboxyl group caries a slight negative charge
The primary structure of a protein is its amino acid sequence:
Primary structure the precise sequence of amino acids in a polypeptide chain held
together by peptide bonds
The secondary structure of a protein requires hydrogen bonding:
Secondary structure consists of regular, repeated patterns in different regions of a
polypeptide chain
Two different structures helix and pleated sheet
The tertiary structure of a protein is formed by bending and folding:
Tertiary structure the polypeptide chain is bent at specific sites and then folded back and
forth
It is unique to every protein
The exposed outer surface present the functional groups capable of interacting with other
molecules in the cell
Covalent disulfide bridges can form between specific cysteine side chains
Hydrogen bonds between side chains stabilize folds in protein
Hydrophobic chains can aggregate together in the interior of the protein, folding the
polypeptide in the process
Ionic attraction can form between positively and negatively charged side chains, forming salt
bridges between amino acids
Denaturized if a protein is heated slowly and moderately, the heat energy will disrupt only
the weak interactions, causing the secondary and tertiary structure to break down.
The quaternary structure of a protein consists of subunits:
Quaternary structure results from the ways in which the tertiary structures bind together
and interact
Shape and surface chemistry contribute to protein function:
The specificity of protein bindings depends on two general properties of proteins shape and the
chemistry of its exposed surface groups
Shape when a small molecule collides with and binds to a much larger protein. If it fits has
to do with the general fit between their three-dimensional shapes
Chemistry the exposed R groups on the surface of a protein permit chemical interactions
with other substances.
Chaperone proteins:
They protect the three dimensional structures of other proteins
They prevent inapropriate interaction and enhance the appropriate ones
Has a cagelike structure that pulls in a polypeptide, causes it to fold into the correct shape
and then releases it
Protein category Protein function
Enzymes Catalyze biochemical reactions
Structural proteins Provide physical stability and movement
Defensive proteins Recognize and respond to nonself substances
Signaling proteins Control physiological processes
Receptor proteins Receive and respond to chemical signals
Membrane transporters Regulate passage of substances across cellular
membranes
Storage proteins Store amino acids for later use
Transport proteins Bind and carry substances within the organism
Gene regulatory proteins Determine the rate of expression of a gene

Pentoses five-carbon sugars. Ribose and deoxyribose are the backbone of nucleic acids RNA and
DNA.
Hexoses six-carbon sugars. Mostly sugars.
Disaccharides, oligosaccharides and polysaccharides are all constructed from monosaccharides that
are covalently bonded together by condensation reactions that from glycosidic linkages
Look at the structure of starch, glycogen and cellulose.
Read page 55
7 types of Lipids(non polar):
1. Fats and oil store energy
2. Phospholipids play important structural roles in cell membranes
3. Carotenoids and chlorophylls help plants capture light energy
4. Steroids and modified fatty acids play regulatory roles as hormones and vitamins
5. Fat in animal bodies serves as thermal insulation
6. A lipid coating around nerves provides electrical insulation
7. Oil or wax on the surfaces of skin, fur, feathers and leaves repels water and prevents
excessive evaporation of water from terrestrial animals and plants.
Triglyceride:
Fats and oils fat if is it solid by room temperature, oil if it is liquid by room temperature
Made up of fatty acids and glycerol
Fatty acid made up of a long nonpolar hydrocarbon chain and an acidic polar carboxyl
group
Glycerol small molecule with three hydroxyl (-OH) groups
Saturated fatty acids all the bonds between the carbon atoms in the hydrocarbon chain are
single bonds all the bonds are saturated with hydrogen atoms, can pack together tightly
due to the straight structure (animal fats)
Unsaturated fatty acids the hydrocarbon chain contains one or more double bonds, has
kinks in the structure so it can't pack together tightly (plant oils)
Read the phospholipids part on page 57
Specialized lipids:
Carotenoids light absorbing pigment. Beta carotene can be broken down into two vitamin
A molecules vitamin A is used to make the pigment cis-retinal which is required for vision
Steroids family of organic compounds whose multiple rings are linked through shared
carbons. Steroid cholesterol is an important constituent of membranes helping maintain
membrane integrity.
Vitamins small molecules that are not synthesized by the human body and must be
acquired from the diet.
Waxes coating that repels water. They are substances that are hydrophobic and plastic or
malleable at room temperature. It's a long saturated chain of fatty acid and a long chain of
alcohol joined together by an ester linkage.
Paragraph 4
Nucleo-:
Nucleotides consists of 3 components: a nitrogen-containing base, a pentose sugar and
one to three phosphate groups.
Nucleosides consist of a pentose sugar, a nitrogenous base (no phosphate group)
Bases are nitrogen-containing biological compounds
Phosphodi-ester linkage:
The pentose sugar in the last nucleotide of the chain and the phosphate on the new
nucleotide undergo a condensation reaction and the bond is called a phosphodiester linkage
Thymine:
Thymine bonds to adenine
It can only bind to adenine because of the binding possibilities for the hydrogen bonds
Transcription Translation
Certain DNA sequences can be copied into RNA Nucleotide sequence in the RNA can then be
used to specify a sequence of amino acids in a
polypeptide chain
Information coded in the sequence of nucleotide Information in RNA is passed to polypeptides but
bases in DNA is passed to a sequence of never the reverse (polypeptide to nucleic acids)
nucleotide bases in RNA
Evolutionary relatedness DNA:
A series of DNA molecules stretches back through the lineage of every organism to the
beginning of biological evolution on earth
Closely related living species have more similar base sequences than species that are more
distantly related
It has been confirmed that many of the evolutionary relationships that had been inferred
previously from more traditional comparisons of body structure, biochemistry and
physiology.
Increasingly scientists turn to DNA analyses to elucidate evolutionary relationships when
other comparisons are not possible or are not conclusive
Nucleotides have other important roles:
ATP acts as an energy transducer in many biochemical reactions
GTP serves as an energy source especially in protein synthesis. It also plays a role in the
transfer of information from the environment to cells
cAMP special nucleotide with an additional bond between the sugar and the phosphate
group. Essential in many processes like actions of hormones and the transmission of
information by the nervous system
nucleotides play roles as carriers in the synthesis and breakdown of carbohydrates and
lipids
Redi's experiment:
one jar contained meat exposed to both air and flies
a second jar was covered with a fine cloth so that the meat was exposed to air but not to flies
the third jar was sealed with a lid so the meat was exposed to neither air nor flies
as he had hypothesized he found flies only were the flies had been previously so life could
not spontaneously come up
Pasteurs experiment:
Microorganisms can arise only from other microorganisms and that an environment without
life remains lifeless.
Life from extraterrestrial sources:
A meteorite from space carried molecules that were characteristic of life on earth people
thought life could have come from outside earth
There is evidence that the heat at the centers of some meteorites may not have been severe
when they entered earth's atmosphere. If this was the case then a long interplanetary trip by
living organisms might have been possible.
Why this could be true:
Scientists took great care to avoid contamination
The amino acids found on the meteorite were not likely to have come from a living organism
on earth
The isotope ratios for carbon and hydrogen in the sugars from the meteorite were different
form the ratios of those elements found on earth
That these substances are found on the meteorites does not mean that they actually carried life
because scientists found it hard to believe that an organism could survive thousands of years of
travelling through space in a meteorite.
Life originated on earth trough chemical substances:
Chemical evolution conditions on primitive earth led to formation of these simple
molecules (prebiotic syntheses) and that these molecules led to the formation of life forms
Miller/Urey:
They set up an experimental "atmosphere" containing the gasses they thought were present
in earth's early atmosphere: hydrogen gas, ammonia, methane gas and water vapor.
The passed an electrical spark through these gasses to simulate lightning, a source of energy
to drive chemical reactions
Cooled the system so the gases would condense and collect in a watery solution
After a week the system contained numerous organic molecules including a variety of amino
acids.
Miller:
Filled test tubes with ammonia gas, water vapor and cyanide
He sealed the tubes and cooled them to -78C
He opened them 27 years later and found amino acids and nucleotide bases
Pockets of liquid water within the ice had allowed high concentrations of the starting
materials to accumulate, thereby speeding up chemical reactions
The cold water within the ice on ancient earth and other celestial bodies may have provided
environments for the prebiotic synthesis of molecules required for the subsequent formation
of simple living systems.
Three ancient environments:
Solid mineral surfaces scientists speculate that the silicates in clay may have catalyzed the
condensation reaction that resulted in organic polymers
Hydrothermal vents deep in the ocean iron and nickel haven shown to catalyze the
polymerization of amino acids in the absence of oxygen
Hot pools at edges of oceans evaporation may have concentrated monomers to the point
where polymerization was favored
RNA:
Read page 72
Experiments description:
They put fatty acids in water
When places in water fatty acids will arrange themselves in a round huddle the hydrophilic
heads pointing outwards
If water becomes trapped inside the huddle a second layer of fatty acids forms lipid
bilayer
 Lipid bilayer has the polar heads of the fatty acids facing both outward and inward, the
nonpolar tails form the interior of the bilayer they resemble living cells they are called
protocells
Only small molecules like sugars and individual nucleotides could pass through the bilayer
Nucleic acids inside the protocells could replicate using the nucelotides from outside
Protocells:
Can act as an organized system of parts, with substances interacting and reacting
It includes an interior that is distinct from the exterior environment
It is capable of self replication
Some ancient cells left a fossil print:
They found a rock of 3.5 million years old that contained what looked like tantalizingly like
contemporary cyanobacteria
Cyanobacteria are believed to have been among the first organisms because they can
perform photosynthesis
They looked for chemical evidence to proof it really had been alive
They found the carbon dioxode isotope that belongs to photosynthesis
They found internal substructures that are characteristics of living systems
Paragraph 5
Cell theory:
Cells are the fundamental units of life
All living organisms are composed of cells
All cells come from preexisting cells
Evolution through natural selection explains the diversity of modern cells
Three important implications about cell theory:
1. Studying cell biology is in some sense the same as studying life
2. Life is continuous
3. The origin of life on earth was marked by the origin of the first cells
Scale of life:
Look at 5.1 the scale of life on page 78
Surface area-to-volume ratio:
As an object increases in volume, its surface area also increases, but not at the same rate
The surface area of the cell determines the amount of substances that can enter it from the
outside environment, and the amount of waste products that can exit to the environment
As a cell grows larger its chemical activity increases faster then it's surface area
The smaller the cell the more easily substances can move from one site to another within the
cell
Cells must be small in volume in order to maintain a large enough surface area-to-volume
ratio and an ideal internal volume
Light versus electron microscopes:
Light microscope Electron microscope
Can be used to visualize living cells Can only be used on vacuum prepared dead cells
Has a better resolution
Difference prokaryotic and eukaryotic:
Prokaryotic Eukaryotic
Does not have a nucleus Has a nucleus
Does not have membrane enclosed internal Has membrane enclosed compartments
compartments organelles
Main features prokaryotic cells:
They are smaller than eukaryotic cells
The plasma membrane encloses the cell, regulating traffic in and out of cell and separating
internal from external
The nucleoid is the region were the DNA is located. DNA is the hereditary material that
controls cell growth, maintenance and reproduction.
The rest of the material enclosed in the plasma membrane is called the cytoplasm. It contains
disolved ions, small molecules and soluble macromolecules such as proteins
Ribosomes are complexes of RNA and proteins. They are sites of protein synthesis where
information is coded for in nucleic acids directs the sequential linking of amino acids to form
proteins.
Specialized features are found in some prokaryotes:
Cell walls
located outside the plasma membrane
The rigidity of cell wall supports the cell and determines its shape.
Some bacteria have another layer the outer membrane.
Some bacteria also have a capsule: slimy layer composed mostly of polysaccharides
Internal membrane
They use photosynthesis and these bacteria have an internal membrane system that contains
molecules needed for photosynthesis.
Other prokaryotes have internal membrane folds that are attached to the plasma
membrane.
These folds may function in cell division or in various energy-releasing reactions.
Flagella
In bacteria the filament of the flagellum is made of flagellin (protein)
A complex motor protein spins the flagellum on its axis a propeller driving the cell along
The flagella causes the motion of the cell if removed the cell does not move
Pili
Hairlike structures made of protein
Are shorter then flagella and used for adherence
Adherence attachment
Conjugative pili (sex pili) help bacteria join to one another to exchange genetic material
Cytoskeleton
Collective name for protein filaments that play roles in cell division or maintaining the shape
of the cell
One protein forms a ring structure constricts during cell division
One protein forms a helical structure extends down the lengths of rod-shaped cells help
maintain their shape
Eukaryotic cells:
Have lengths or diameters of usually ten times greater than the prokaryotes
They also have a plasma membrane, cytoplasm and ribosomes
They have organelles
They have a cytoskeleton composed of protein fibers
And an extracellular matrix outside the cell membrane
Microscopy Cell fractionation
Function of organelles could be inferred by Process permits cell organelles and other
observations and experiments cytoplasmic structures to be separated from
each other and examined using chemical
methods
Use of stains targeted to specific Begins with destruction of the plasma
macromolecules allowed the biologists to membrane allows cytoplasmic components to
determine the chemical composition of flow out into a test tube
organelles
Organelles can then be separated on the basis of
size and density
Nucleus:
It is the location of most of the cell's DNA and the site of DNA replication
The site where gene transcription is turned on or off
Region within nucleus nucleolus where ribosomes begin to be assembled from RNA and
proteins
Nuclear envelope integrated structure compromised of two membranes surrounding the
nucleus separates DNA transcription from translation
Pores regulate traffic between nucleoplasm and cytoplasm
Ions and small molecules can diffuse trough the pores have to weigh less than 10,000
Larger molecules can only get through if they have a specific short sequence of amino acids
RER SER
Many ribosomes attached to outer surface Has no ribosomes
Receives newly synthesized proteins and Some proteins that came from the RER are
segregates them from the cytoplasm modified with the lumen of the SER
participates in transporting them
Proteins can be chemically modified to alter Responsible for chemical modification of small
their function and tag them for delivery to molecules make the targeted molecules more
specific cellular destinations polar
Most membrane-bound proteins are made here The site for glycogen degradation
Lipids and steroids are synthesized here
Stores calcium ions when they are released
they trigger cell responses
Golgi apparatus:
Receives protein-containing vesicles from RER
Modifies, concentrates, packages and sorts proteins before they get sent to their
destinations
Adds carbohydrates to proteins and modifies other carbohydrates that were attached to
proteins in the RER
Some polysaccharides the plant cell wall are synthesized
Look at 5.10 on page 91
Lysosomes:
Are sites for the breakdown of food, other cells or foreign objects that are taken up by the
cell
Phagocytosis a pocket forms in the plasma membrane and then deepens and encloses
material from outside the cell, pocket becomes a small vesicle called phagosome which
breaks free of plasma membrane to move into cytoplasm. There it fuses with another
lysosome in which digestion occurs
The enzymes in the second lysosome hydrolyze the food particles and the products of
digestion pass through the membrane of lysosome to provide energy and raw materials for
other cellular processes
 the second lysosome with the undigested particles moves to the plasma membrane, fuses
with it and releases the undigested content to the environment
autophagy programmed destruction of cell components
Mitochondrion:
molecules that result from the partial degradation enter the mitochondria
primary function harvest the chemical energy of fuel molecules that the cell can use
namely ATP
cellular respiration the production of ATP in the mitochondria using fuel molecules and
molecular oxygen
cells that are active in movement and growth require the most chemical energy and these
tend to have the most mitochondria per unit volume
Mitochondria have two membranes outer membrane is smooth and protective + offers
little resistance. You also have the inner membrane which folds inward in many places and
thus has a greater surface area
in the inner membrane are many large protein complexes that participate in cellular
respiration
mitochondrial matrix space enclosed by the inner membrane, contains ribosomes and
DNA which are used to make some of the proteins needed for cellular respiration
Plastids
Chloroplast:
contains chlorofyll and is the site of photosynthesis
photosynthesis is the energy source for most of the living world
it's surrounded by two membranes and there is a series of internal membranes whose
structure and arrangement vary from one group of photosynthetic organisms to another
the internal membranes of chloroplasts look like stacks of flat hollow pita bread-like
compartments called thylakoids
other types of plastids such as chromoplasts and leucoplasts have functions different from the
chloroplasts. Chromoplasts for example make and store, red, yellow and orange pigment in flowers
and fruits

peroxisomes:
small organelles that accumulate toxic peroxides (like HO) that occur as by-products of
some biochemical reactions
have a single membrane and a granular interior containing specialized enzymes
glyoxysomes:
similar to peroxisomes but only found in plants
are locations where stored lipids are converted into carbohydrates for transport to growing
cells
Vacuoles: the four main functions:
1. storage plant cells produce a number of toxic by-products and waste products, many of
which are simply stored within vacuoles
2. structure presence of dissolved substances in vacuole causes water to enter it from the
cytoplasm making the vacuole swell. A mature plant cell does not swell when the vacuole fills
with water but instead it stiffens which is called turgor
3. reproduction the pigments that are in the vacuole are visual cues which help attract
animals that assist in pollination or seed dispersal
4. digestion some vacuoles contain enzymes that hydrolyze stored proteins into monomers.
During seed germination the monomers are used as food by the developing plant seedlings
there are three components of a eukaryotic cytoskeleton: microfilaments, intermediate filaments
and microtubulus
Microfilaments:
can exist as a single filament, in bundles or networks and are about 7 nanometers in
diameter
they help the entire cell or parts of the cell move
they determine and stabilize cell shape
are assembled from omnomers of actin
Intermediate filaments:
50 different kinds and many of them specific to a few cell types and they fall into six
molecular classes
Tough, ropelike protein assemblages 8-12 nanometer in diameter
They anchor cell structures in place
The resist tension
Microtubulus:
Long, hollow, unbranched cylinders about 25 nanometers in diameter
They form a rigid internal skeleton for some cells
They act as framework along which motor proteins can move structures within the cell
Cilia and flagella movable appendages on eukaryotic cells
Plant cell wall:
Provides support for the cell and plant by remaining rigid, but still be flexible enough so the
plant can move in for example the wind
It acts as a barrier to infection by fungi and other organisms that can cause plant disease
It contributes to plant form by growing as the plant cells expand
Cytoplasm and adjacent plant cells are connected by numerous plasma membrane-lined
channels called plasmodesmata
Plasmodesmata permit diffusion of water, ions, small molecules, RNA and proteins
between connected cells, allowing for the use of these substances far from their sites on
synthesis
Extracellular matrix:
Is composed of three types of molecules: collagen (fibrous molecules), proteoglycans and a
third protein group that links them all together
It holds the cell together in tissues
It contributes to the physical properties of cartilage, skin and other tissues
It helps filter materials passing between different tissues
It helps orient cell movements during embryonic development and during tissue repair
It plays a role in chemical signaling from one cell to another
Endosymbiosis theory:
1. Some organelles (mitochondria and plastids) are not by infolding of the plasma membrane
but by one cell ingesting another cell
2. The ingested cell lost its autonomy and some of its function
3. Many of the ingested cell's genes were transferred to the host's DNA
4. Mitochondria and plastids in today's eukaryotic cells are the remnants of these symbionts,
retaining some specialized functions that benefit their host cells