Description
Chapter 1: The Science of Biology
Scientific Method
Biology is studied using the scientific method
Science is based on a systematic thought process
∙ Deductive and inductive reasoning
Deductive reasoning: summarizes the information at hand, draw conclusions from that information and proceeds from the general to the specific. Based on this, if starting general assumptions are true, then the conclusion must be true. Example: All birds have wings, sparrows are birds. Deduced conclusion would be: sparrows have wings.
Inductive reasoning: draws generalization from several specific observations and proceeds from the specific to the general; must be careful because it is impossible to prove the accuracy of the
generalization. Example: Sparrows are birds, and they have wings. Falcons are birds, and they have wings. In fact, all birds that I have ever seen or heard of have wings. Induced conclusion would be: All birds have wings.
Forms basis of most science
In a nutshell, scientific method summarizes existing observations, makes a model about how the universe works using those observations, tests the model. And revise the model as needed and repeat. Don't forget about the age old question of What is the difference between introns and exons?
Summarizing existing observations may also involve collecting new information if there aren’t enough
Then a hypothesis is made; this is a testable model that explains the existing observations, makes predictions that can be tested. To test the correctness of the hypothesis, an experiment is conducted.
Experimental or treatment group: the individuals given the specific treatment or condition being tested
Control group: the individuals not given the specific treatment Observations and measurements are taken of the treatment and control groups whereby the data are compared, and they should provide evidence to either reject or support the hypothesis
Care must be taken that the treatment and control groups receive the same treatments except for the specific effect being tested. Example: the placebo effect.
Analysis of experiments
∙ Experimenter must interpret the results
∙ Taking small sample sizes often results in errors in the estimate of the entire population, so the larger the sample size, the more reliable the resultsWe also discuss several other topics like What is the key formula you should use in price elasticity of demand?
∙ The recursive nature of the process: experiments provide more observations, at any time observations may be added in and more testable models may be produced; this may in turn lead to more experiments, and the process continues. This generally leads to progress towards more and more reliable models of how nature works. Don't forget about the age old question of What is the definition of market segment?
Hypothesis, theory, and law We also discuss several other topics like What is the study of matter?
∙ A well supported hypothesis that links together a large body of observations is considered a theory
∙ A theory that links together significant bodies of thought and yields unvarying and uniform prediction over a long period of time becomes considered a principle or law
Scientific Method
∙ Caveats: scientific models can only be proven false, never proven true ∙ The supernatural cannot be tested scientifically, thus, it is outside the realm of science Don't forget about the age old question of Define classical conditioning.
∙ Science and technology-the goal of science is to understand nature; the goal of technology is to apply scientific knowledge for a specific purpose
Characteristics of Living Matter
∙ Living things are made up of cells
A cell is the basic unit of life, both in structure and function; it is living material bounded by a membrane. It comes from and give rise to other cells
Some are unicellular-organism consisting of a single cell
Some are multicellular-organism consisting of more than one cell ∙ All living things grow and develop
Growth-increase in size and number of cells; may be different in different locations
Development-changes in roles of cells during life cycle of an organism; individual changes as development proceed throughout life
∙ Living things regulate their metabolism
∙ Metabolism-the sum of the chemical reactions and energy
transformations that take place within a cell
∙ Homeostasis- the tendency of an organism to maintain a relatively constant internal environment. Don't forget about the age old question of Define amplitude.
Living things perceive and respond to stimuli
Stimulus-physical or chemical changes in the internal or external environment of an organism
∙ Living things reproduce
∙ Reproduction can be asexual (copying):
o Does not involve sex (genetic recombination); variation only by mutation in genes
o Simple-cells split
∙ Reproduction can be sexual
Sex (genetic recombination)
Complex, involves fusion of specialized egg and sperm cells to form a zygote (fertilized egg)
Information transfer in living systems
Information must be transferred from one cell generation to the next Cells have an information system made up of nucleic acids-specifically: DNA (deoxyribonucleic acid)
The information is encoded in regions of DNA called genes, the units of heredity; they are instructions that use a special, unique code which are generally to produce specific proteins
In multicellular organisms, information must also be transferred from a generation to the next
Information is also exchanged between cells
Hormones are chemical signals used for intercellular signaling Physical signals may also be used for intercellular communication, e.g. nerve cells
Diversity of life/classification of living systems
Biologists use a binomial system for classifying organisms
Taxonomy-the science of classifying and naming organisms
Carolus Linnaeus-18th century Swedish botanist; developed a system of classification that is the basis of what is used today
Binomial system because a combination of two names, genus and specific epithet, uniquely identifies each species
Species-basic unit of classification or taxonomy
If sexual, a group of organisms that can interbreed and produce fertile offspring
If asexual, grouped based on similarities (DNA sequence is best) About 1.8 million living species have been described, likely millions more
Genus-a group of closely related species
Species name has two parts (binomial)
∙ Genus name is always capitalized, and the specific epithet is never capitalized
∙ The genus and specific epithet are always together, and italicized or underlined; example: Homo Sapiens or Homo sapiens
Taxonomic classification is hierarchical
A group of related genera make up a Family
Related families make up an order
Related orders are grouped into a class
Related classes are grouped into a phylum or division
Related phyla or divisions are grouped into a kingdom
Related kingdoms are grouped into a domain, the highest level of classification in the modern system
The gold standard for “related” is based on DNA sequence similarities
The most widely accepted classification system today includes three domains and six kingdoms
Two domains consist of prokaryotes, organisms with no true cellular nucleus
Domain Archaea-kingdom Archaebacteria
bacteria typically found in extreme environments
distinguished from other bacteria mainly by ribosomal RNA sequence
include methanogens, extreme halophiles, and extreme
thermophiles
Domain bacteria-kingdom eubacteria
∙ very diverse group of bacteria; examples: blue-green algae, Escherichia coli
Domain eukarya,
o eukaryotes, organisms with a discrete cellular nucleus; divided into four kingdoms:
∙ Kingdom Protista
o Single celled and simple multicellular organisms having nuclei o Includes protozoa, algae, water molds, and slime molds
o “Lump group”
∙ Kingdom Fungi
o Organisms with cell walls consisting of chitin
o Mostly multicellular, multi-tissued
o Includes molds, yeasts, mushrooms, etc. that are mostly decomposers ∙ Kingdom Plantae
Plants are complex multicellular organisms having tissues and organs They have cell walls containing cellulose
Most contain chlorophyll in chloroplasts, and carry on the process of photosynthesis
Nonvascular (mosses), and vascular (ferns, conifer, flowering plants) Kingdom is replaced by Viridiplantae, which includes green algae Kingdom Animalia
Complex multicellular organisms that depend on other organisms for nourishment
No cells wall
Have organs and organ systems
Most forms are motile
Energy flow in living systems
Energy is used to maintain existing cellular structures and components (replacement of damaged or worn out materials within the cell)
Used to produce materials to support growth, development, and reproduction Used to support:
∙ Movement, either of cell itself or of materials into and out of the cell ∙ Signaling responses, such as hormone production and perception, nerve impulses.
∙ Other forms of cell work, such as symbiotic relationships with other organisms, defense against pathogens
Energy flows through ecosystems (food chain or food web)
Producers (autotrophs) manufacture their own food from simple materials usually produce food by the process of photosynthesis:
o Carbon dioxide +water +light energy = carbohydrate (food) + oxygen
Use such food by oxidative respiration
Carbohydrate (food) +oxygen = carbon dioxide + water +energy Overall, producers use carbon dioxide and water and release food and oxygen
Consumers (heterotrophs) obtain energy by eating other organisms (ultimate source of food is producers); use food and oxygen, and release carbon dioxide and water
Decomposers obtain energy by breaking down the waste products, by products, and dead bodies of producers and consumers. Usually bacteria and fungi.
Themes
The cell
Information management
Heritable information
Regulation
Interaction with the environment
Energy management
Structure and function
Unity and diversity
Emergent properties
Evolution: the core unifying theme that explains much of the observations connected with the other themes
In addition, an awareness of the process of scientific inquiry and the application of science (technology) are important aspects of any study of biology.
Chapter 2: Chemistry
Elements and Atoms
Elements: substances that cannot be further broken down into other substances (at least by ordinary chemical reactions)
Every element has a chemical symbol
There are 92 naturally occurring elements, from hydrogen up to uranium
∙ O, C, H, N make up approximately 96% of living mass
∙ Ca, P, K, S, Na, Cl, Mg, Fe-consistently present in small
amounts
∙ Several trace elements
Atom is the smallest unit of an element
Electron: little mass; -1 electrical charge
Proton: approximately 1 mass unit; +1 electrical charge
Neutron: approximately 1 mass unit; no electrical charge
Nucleus: protons and neutrons
Atomic number: number of protons
Periodic table arranged largely according to atomic number
Atomic mass=protons + neutrons
Isotopes: numbers of protons are the same, number of neutrons are different
Atomic nuclei can undergo changes (decay)
o Some elements are more stable than others
o Some isotopes are more stable than others (most unstable = radioisotopes)
o Decay rates are statistical averages; used for measuring time passage in many areas of science (carbon dating, etc.)
o The radiation emitted upon decay (alpha, beta, and/or gamma) can be used as a tool for experiments; can also be used medically; has other uses and dangers (nuclear power, nuclear bombs, radiation poisoning.)
o Radiation can cause mutations in DNA, can interfere with cell division Electrons occupy orbitals surrounding the nucleus
o Atoms: numbers of electrons are the same as number of protons o Orbitals: electrons energy levels, location probabilities
The further away an orbital carries an electron from the nucleus, the higher the energy level of the electron
o Electron shell: orbitals with similar energies
The outer electrons are known as the valence electrons which are involved in chemical interactions “rule of eight”; collectively, they occupy the valence shell that is filled by highest-energy electrons
The chemical properties of an atom are largely determined by the valence electrons
The science of chemistry mostly involves study of how electrons move about the nucleus, store energy, and determine chemical properties of substances as a result
Describing Atomic Combinations
Atoms combine to form molecules and compounds
∙ Molecule: two or more atoms held together by covalent bonds o Smallest unit of a molecular substance
o Differs in properties from its elements
o Not all substances are molecular
∙ Compound: specific combination of two or more different elements chemically in a fixed ratio
Differs in properties from its elements
May have ionic bonds
Some compounds are held together by covalent bonds and
therefore molecular
Chemists use two types of formulas to describe substances
o Chemical formula: number of atoms of each element
Molecular formula if a molecule is involved
Simplest ratio for ionic compounds (NaCl, etc.)
o Structural formula: arrangements of atoms in a molecule
Examples:
Water H-O-H
Carbon dioxide O=C=O
Molecular oxygen O=O
The number of units of a substance are described using the mole Molecular mass: sum of the atomic masses of the atoms in the molecule Mole: number of molecules for gram amount to is the same as the atomic mass
o Example: water has molecular mass 1+1+16=18
Mole of water has a mass of 18g
Mole is simply a conversion factor
o Avogadro’s number, is 6.02 x 10^23 atoms or molecules
Chemical bonds hold molecules together and store energy
Recall that electrons in the outermost shell of an atom (valence electrons) determine the chemical behavior of the atom, i.e. what type and how many chemical bonds it can readily form
Most atoms in biological systems seek 8 electrons in their outermost shell (hydrogen seeks 0 or 2 electrons in its outermost shell)
Since atoms have the same number of electrons as protons, they meet this need to have a full valence shell by sharing, giving up, or acquiring electrons from any other atoms; this form chemical bonds
Chemical bonds are based on filling valence shells
o Reduced energy state
o Bond energy is the amount of energy required to break a chemical bond
Strong chemical bonds
o Covalent bonds: electrons shared
Result in filled valence shells
Electrons are shared in pairs
1 pair is a single covalent bond
Double and triple also possible
Carbon forms four total
Give molecules definite shapes
Represented by solid lines
The shared atomic orbitals require definite spatial arrangements that depend on the atoms involved in the bond
Nonpolar: equal sharing
Polar: unequal sharing
∙ Polar if one nucleus holds a stronger attraction on the
electron pair
∙ Polar molecules have regions with partial charges
Ionic bonds: ions of opposite charge
Ion: atom that has gained or lost at least one net electron
o Cations: lost one or more; + charge
Anions: gained one or more; - charge
-ide indicates an anion
Polyatomic ions can also form
o Covalently bound atoms that loss or gain electrons or protons o Only polyatomic ions can lose or gain protons
o Polyatomic cations=positive charge; polyatomic anions= negative charge
∙ Ionic bond: cation/anion attraction
o Ionic compound: substance with ionic bonds
Ionic compounds dissociate into individual ions when dissolved in a polar substance, such as water
o Hydration: surrounding the ions with the ends water molecules with the opposite (partial) charge
o Very important in many processes such as photosynthesis. Respiration, more
Electrons are less easily lost from molecules than from atoms o Molecules typically will lose the equivalent of a complete hydrogen atom when oxidized (proton as well as electron)
o Counting charge changes alone is not sufficient-look for movement of electrons, includes complete H equivalent.
Video notes
Energy levels of an atom’s electrons
Diagram shows the model of an atom with the nucleus at the center and electrons around it.
Electrons move rapidly around the nucleus according to how much energy they have
The electron energy levels called electron shells are shown as flat circles around the nucleus, but they are in 3-dimensions, so each circle represents aa spherical region around the nucleus.
Only a section is shown, electrons can have different amounts of energy depending on how fast they are moving and how far they are from the nucleus
Each shell represents different amount of potential energy that an electron can have.
Electrons with the lowest potential energy spend their time in the first electron shell, closest to the nucleus; the negatively charged electrons are attracted to the positively-charged nucleus, but they never fall into it because of their momentum.
The farther an electron shell is from the nucleus, the higher the potential energy of the electrons in that shell.
Electrons can only contain certain amounts of potential energy Why does an electron need to absorb energy to move out to a higher shell? Because it needs energy to pull away from the attraction of the nucleus. The energy might come from a photon of light, or another energy source that delivers the exact amount of energy to boost the electron out to a higher shell.
An electron that is been boosted to a higher potential energy level an exited electron. Electron doesn’t stay long before they move back to lower shells giving off energy in the process.
How much potential energy will an electron lose as it drops down from shell 3 to shell 2?
As excited electrons drop down to shells of lower potential energy, they release the same amount of energy that they absorbed to move out to the higher shell in the first place. Energy lost is often given off as heat.
How electrons boosted to higher potential energy states by sunlight are used to drive photosynthesis, a process essential to all life on earth
Video 2 notes
Electronegativity is the tendency for an atom to pull electrons toward itself. Two atoms of the same element have equal electronegativities; in a covalent bond, they share electrons equally, forming a nonpolar covalent bond.
Atoms in a molecule do not always share electrons equally. More electronegative elements attract electrons more strongly
Chapter 4
Life is based on molecules with carbon (organic molecules)
Much of the chemistry is based on organic compounds
Organic compounds have at least one carbon atom covalently bound to either: another carbon atom or to hydrogen; the chemistry of organic molecules is organized around the carbon atom
Carbon atoms have six electrons-2 in level 1, and 4 in their valence (outer) shell (level 2)
o Carbon is not a strongly electron seeking element, and it does not readily give up its electrons. Thus, carbon does not readily from ionic bonds. It almost always shares electrons, forming covalent bonds
o Carbon can form up to 4 covalent bonds (and typically does form all four)
Wide diversity in organic compounds
o Over 5 million identified
o Variety partially because carbon tends to bond to carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphorus
Hydrocarbons-contain only hydrogen and carbon
Single carbon-carbon bonds allow rotation around them
and lend flexibility to molecules
o Building of organic macromolecules also leads to diversity
Carbon works well as a molecular “backbone” for forming long
chain molecules due to the number and strength of its bonds,
particularly carbon-carbon bonds
Stronger carbon-carbon bonds can be made with double and
triple covalent bonds
Carbon chains can branch
The shape of a molecule is important in determining its chemical and biological properties
o The 4 bonds formed by carbon are formed at 109.5-degree angles from each other and form a pyramid with a triangular base called a
tetrahedron
o When double bonds are formed the bonds are formed at angles 120 or 180 degrees apart, and they all lie in the same plane
o These bond angles for carbon play a critical role in determining the shape of molecules
o Generally, there is freedom to rotate around carbon to carbon single bonds, but rotation around double bonds is not permitted
o Cis-trans isomers
∙ Diastereomers associated with
compounds that have carbon-carbon
double bonds
∙ Since there is no rotation around the
double bond the other atoms attached to
the carbons are stuck in place in
relationship to each other
∙ Larger items together= cis; larger items
opposite=trans
∙ Examples: trans-2-butene and cis-2-
butene
o Enantiomers: substances that are mirror images of
each other and that cannot be superimposed on each
other
Sometimes called optical isomers
Typically, only one form of an enantiomer pair is
found in and/or used by organisms
The enantiomers are given designations such as
[(+)- vs. (-)-] or [D- vs. L-] or [(R)- vs. (S)-]
Biologically important enantiomers include
∙ Amino acids (found in proteins)-most are
L- amino acids (e.g. L-leucine, L-alanine,
etc.)
∙ Sugars-most are D-sugars (e.g. D-glucose,
D-fructose, etc.)
o Maltose (malt sugar): two glucose subunits
o Sucrose (table sugar): glucose + fructose
o Lactose (milk sugar): glucose + galactose
1. Polysaccharides are macromolecules made of repeating monosaccharides units linked together by glycosidic bonds Number of subunits varies, typically thousands
Can be branched or unbranched
Some are easily broken down and are good for energy storage (examples: starch, glycogen)
Some are harder to break down and are as good as structural components (examples: cellulose)
Starch: main energy storage carbohydrate of plants o Polymer made from α-glucose units linked primarily between carbons 1 and 4
o Amylose: unbranched starch chain (only have α1-4 linkages)
o Amylopectin: branched starch chain (branches by
linkages between carbon 1 and 6)
o Plants store starches in organelles called
amyloplasts, a type of plastid
Glycogen: main energy storage carbohydrate of animals o Like starch, but very highly branched and more
water-soluble
o Is NOT stored in an organelle; mostly found in liver and muscle cells
Cellulose: major structural component of most plant cell walls o Polymer made from β-glucose units linked primarily between carbons 1 and 4 (like starch, but note that
the β1-4 linkage makes a huge difference)
o Unlike starch, most organisms cannot digest
cellulose
o Cellulose is a major constituent of cotton, wood,
and paper
o Cellulose contains approximately 50% of the carbon in found in plants
o Fibrous cellulose is the “fiber” in your diet
o Some fungi, bacteria, and protozoa make enzymes that can break down cellulose
o Animals that live on materials rich in cellulose, e.g. cattle, sheep, and termites, contain microorganisms
in their gut that can break down cellulose for use
by the animal
1. Because of this character phospholipids are important constituents of biological membranes
A. Terpenes are long-chained lipids built from 5-carbon isoprene units 1. Many pigments, such as chlorophyll, carotenoids, and retinal, are terpenes or modified terpenes (often called terpenoids)
2. Other terpenes/terpenoids include natural rubber and “essential oils” such as plant fragrances and many spices
3. Steroids are terpene derivatives that contain four rings of carbon atoms
∙ Side chains extend from the rings; length and structure of the side chains varies
∙ One type of steroid, cholesterol, is an important
component of cell membranes
∙ Other examples: many hormones such as testosterone, estrogens
Chapter 6
A tour of the cell
I. Cell theory
A. All living organisms are composed of cells
a. Smallest “building blocks” of all multicellular organisms
b. All cells are enclosed by a surface membrane that separates them from other cells and from their environment
c. Specialized structures with the cell are called organelles; many are membrane- bound
B. Today, all new cells arise from existing cells
C. All presently living cells have a common origin
a. All cells have basic structural and molecular similarities
b. All cells share similar energy conversion reactions
c. All cells maintain and transfer genetic information in DNA
d. The genetic code is essentially universal
II. Cell organization and homeostasis
A. Plasma membrane surround cells and separates their contents from the external environment
B. Cells are heterogenous mixtures, with specialized regions and structures (such as organelles)
C. Cell size is limited
a. Surface area to volume ratio puts a limit on cell size
i. Food and/or other materials must get into the cell
ii. Waste products must be removed from the cell
iii. Thus, cells need a high surface area to volume Ratio,
but volume increases faster than surface area as cells
grow larger
b. Cell shape varies depending both on function and surface area requirements
III. Studying cells-microscopy and fractionation
A. Most cells are large enough to be resolved from each other with light microscopes (LM)
Cells were discovered by Robert Hooke in 1665; he saw
the remains of cell walls in cork with a LM, at about 30x
mag
Modern LMs can reach up to 1000x
LM resolution (clarity) is limited about 1micrometer due to the wavelength of visible light (only about 500 times
better than the human eye, even at maximum
magnification)
Small cells (such as most bacteria) is about 1 micrometer across, just on the edge of resolution
Some modifications of LMs and some treatments of cells
allow observation of subcellular structure in some cases
B. Resolution of most subcellular structure requires electron microscopy (EM)
a. Electrons have a much smaller wavelength than light (resolve down to under 1nm)
b. Magnification up to 250,000x or more and resolution over 500,000 times better than the human eye
c. Includes transmission (TEM) and scanning (SEM) forms
i. Transmission-electron passes through sample; need very
thin samples (100nm or less thick); samples embedded in
plastic and sliced with a diamond knife
ii. Scanning -samples are gold-plated; electrons interact with the surface; images have a 3-D appearance
C. Cells can be broken and fractionated to separate cellular components for study
Cells are broken (lysed) by disrupting the cell membrane, often using some sort of detergent
Grinding and other physical force may be required, especially if cell walls are present
Centrifugation is used to separate cellular components
o Using a centrifuge, samples are spun at high
speeds, resulting in exposure to a centrifugal force
of thousands to hundreds of thousands of times
“normal” gravity (example, 500,000 x G)
o Results in a pellet and supernatant after spinning;
cell components will be in one or the other
depending on their individual properties; intact
membrane-bound organelles often wind up in
pellets, depending on their density and the
centrifugal force reached (denser = more likely in
pellet)
o Special treatments can determine whether a
compound ends up in pellet or supernatant
o Density gradients can be used to subdivide pellet
compounds based on their density; this can be
used to separate similar organelles from each
other, for example Golgi apparatus from ER
IV. Eukaryotic vs. prokaryotic cells
a. Eukaryotic cells have internal membranes and a distinct, membrane enclosed nucleus; typically, 10-100 micrometer in diameter
b. Prokaryotic cells do not have internal membranes (thus no nuclear membrane)
i. Main DNA molecule (chromosome) is typically circular; is
location is called the nuclear area
ii. Other small DNA molecules (plasmids) are often present, found throughout the cell
iii. Plasma membrane is usually enclosed in a cell wall that is often covered with a capsule (layers of proteins and/or sugars)
iv. Do not completely lack organelles; the plasma membrane and the ribosomes are both present and are considered organelles v. AKA bacteria, prokaryotic cells are typically 110 micrometers in diameter
V. Compartments in eukaryotic cells (cell regions, organelles) A. Two general regions inside the cell: cytoplasm and nucleoplasm a. Cytoplasm-everything outside the nucleus and within the plasma membrane; contains fluid cytosol and organelles
b. Nucleoplasm-everything within the nuclear membrane
B. Membranes separate cell regions
a. Have nonpolar regions that help form a barrier between aqueous regions
b. Allow for some selection in what can cross a membrane (more details later)
VI. Nucleus- the “control center” of the cell
A. Typically, large (approximately 5 micrometer) and singular B. Nuclear envelope
a. Double membrane surrounding the nucleus
b. Nuclear pores- protein complexes that cross both membranes and regulate passage
C. Chromatin-DNA protein complex
a. Have granular appearance; easily stained for microscopy
(“chrom-“= color)
b. “Unpacked” DNA kept ready for message transcription and DNA replication
c. Proteins protect DNA and help maintain structure and
function
d. Chromosomes- condensed or “packed” DNA ready for cell division (“-some” = body)
D. Nucleoli-regions of ribosome subunit assembly
a. Appears different due to high RNA and protein concentration (no membrane)
b. Ribosomal RNA (Rrna) transcribed from DNA there
c. Proteins (imported from cytoplasm) join with Rrna at a
nucleolus to form ribosome subunits
d. Ribosome subunits are exported to the cytoplasm through nuclear pores
VII. Ribosomes-the sites of protein synthesis
A. ribosomes are granular bodies with three RNA strands and about 75 associated proteins
a. two main subunits, large and small
b. perform the enzymatic activity for forming peptide bonds, serve as the sites of translation
B. prokaryotic ribosome subunits are both smaller than the
corresponding subunits in eukaryotes
C. in eukaryotes
a. the two main subunits are formed separately in the nucleolus and transported separately to the cytoplasm
b. some are free in the cytoplasm while others are associated with the endoplasmic reticulum (ER
VIII. endomembrane system- a set of membranous organelles that interact with each other via vesicles
A. includes ER, Golgi apparatus, vacuoles, lysosomes, microbodies, and in some definitions the nuclear membrane and the plasma membrane
B. endoplasmic reticulum (ER)-membrane network that winds through the cytoplasm
a. winding nature of the ER provides a lot of surface area
b. many important cell reactions or sorting functions require ER membrane surface
c. ER lumen-internal aqueous compartment in ER
i. Separated from the rest of the cytosol
ii. Typically, continuous throughout ER and with the
lumen between the nuclear membranes
iii. Enzymes within lumen and imbedded in lumen side of
ER differ from those on the other side, thus dividing
the functional groups
d. Smooth ER-primary site of lipid synthesis, many
detoxification reactions, and sometimes other activities
e. Rough ER-ribosomes that attach there insert proteins into the ER lumen as they are synthesized
i. Ribosome attached directed by a signal peptide at the
amino end of the polypeptide
1. A protein/RNA signal recognition particle (SRP)
binds to the signal peptide and pauses
translation
2. At the ER the assembly binds to an SRP receptor
protein
3. SRP leaves, protein synthesis resumes (now into
the ER lumen), and the signal peptide is cut off
ii. Proteins inserted into the ER lumen may be membrane bound or free
iii. Proteins are often modified in the lumen (example, carbohydrates or lipids added)
iv. Proteins are transported from the ER in transport
vesicles
C. Vesicles-small, membrane-bound sacs
a. Buds off an organelle (ER or other)
b. Contents within the vesicles (often proteins) transported to another membrane surface
c. Vesicles fuses with membranes, delivering contents to that organelle or outside of the cell
D. Golgi apparatus (AKA Golgi complex)- a stack of flattened membrane sacs (cisternae) where proteins further processed, modified, and sorted [the “post office” of the cell]
a. Not contagious with ER, and lumen of each sac is usually separate from the rest
b. Has three areas: cis, medial, and trans
i. Cis face: near ER and receives vesicles from it; current model (cisternal maturation model) holds that vesicles coalesce to continually form new cis cisternae
ii. Medial region: as a new cis cisterna is produced, the older cisternae mature and move away from the ER
1. In this region proteins are further modified
(making glycoproteins and/or lipoproteins where
appropriate, and)
2. Maturing cisternae may make other products;
for example, many polysaccharides are made in
the Golgi
3. Some materials are needed back the new cis
face and are transported there in vesicles
iii. Trans face: nearest to the plasma membrane; a fully matured cisterna breaks into many vesicles that are
set up to go to the proper destination (such as the
plasma membrane or another organelle) taking their
contents with them
E. Lysosomes-small membrane-bound sacs of digestive enzymes a. Serves to confine the digestive enzymes and their actions b. Allows maintenance of a better pH for digestion (often
about pH 5)
c. Formed by budding from the Golgi apparatus; special sugar attachments to hydrolytic enzymes made in the ER target them to the lysosome
d. Used to degrade ingested material, or in some cases dead or damaged organelles
i. Ingested material is found in vesicles that bud in from
the plasma membrane; the complex molecules in
those vesicles is then digested
ii. Can also fuse with dead or damaged organelles and
digest them
e. Digested material can then be sent to other parts of the cell for use
f. Found in animals, protozoa; debatable in other eukaryotes, but all must have something like a lysosome
F. Vacuoles-large membrane-bound sacs that perform diverse roles; have no internal structure
a. Distinguished from vesicles by size
b. In plants, algae, and fungi, performs many of the roles that lysosomes perform for animals
c. Central vacuole-typically a single, large sac in plant cells that can be 90% of the cell volume
i. Usually formed from fusion of many small vacuoles in
immature plant cells
ii. Storage sites for water, food, salts, pigments, and
metabolic wastes
iii. Important in maintaining turgor pressure
iv. Tonoplast- membrane of the plant vacuole
d. Food vacuoles-present in most protozoa and some animal cells; usually bud from lysosomes for digestion
e. Contractile vacuoles-used by many protozoa for removing excess water
G. Microbodies-small membrane -bound organelles that carry out specific cellular functions; examples:
a. Lysosomes could be considered a type of microbody
b. Peroxisomes-sites of many metabolic reactions that produce hydrogen peroxide ( H2O2 ), which is toxic to the rest of the
cell
i. Peroxisomes have enzymes to break down H2 O2 ,
protecting the cell
ii. Peroxisomes are abundant in liver cells in animals and
leaf cells in plants
iii. Normally found in all eukaryotes
iv. Example: detoxification of ethanol in liver cells occurs
in peroxisomes
c. Glyoxysomes-in plant seeds, contains enzymes that convert stored fats into sugar
IX. Energy converting organelles
A. energy obtained from the environment is typically chemical energy (in food) or light energy
B. mitochondria are the organelles where chemical energy is placed in a more useful molecule, and chloroplasts are plastids where light energy is captured during photosynthesis
C. mitochondria-the site of aerobic respiration
a. recall aerobic respiration: sugar +oxygen → carbon dioxide
+ water+ energy
b. the “energy” is stored in ATP
c. mitochondria have a double membrane
i. space between membranes= intermembrane space ii. inner membrane is highly folded, forming cristae;
provides a large surface area
iii. inner membrane is also a highly selective barrier
iv. the enzymes that conduct aerobic respiration are
found in the inner membrane
v. inside of inner membrane is the matrix, analogous to the cytoplasm of a cell
d. mitochondria have their own DNA, and are inherited from the mother only in humans
e. mitochondria have their own division process, like cell division; each cell typically has many mitochondria, which can only arise from mitochondrial division
f. some cells require more mitochondria than others g. mitochondria can leak electrons into the cell, allowing toxic free radicals to form
h. mitochondria play a role in initiating apoptosis (programmed cell death)
D. plastids-organelles of plants and algae that produce and store food a. include amyloplasts (for starch storage), chromoplasts (for color, often found in petals and fruits), and chloroplasts (for photosynthesis)
b. like mitochondria, have their own DNA (typically a bit larger and more disk-shaped than mitochondria, however)
c. derive from undifferentiated proplastids, although role of mature plastids can sometimes change
d. numbers and types of plastids vary depending on the organism and the role of the cell
e. chloroplasts get their green color from chlorophyll, the main light harvesting pigments involved in photosynthesis (carbon dioxide +water + light energy → food (glucose) + oxygen)
f. chloroplasts have a double membrane
i. the region within the inner membrane is the stroma; it is analogous to the mitochondrial matrix
ii. inner membrane is contiguous with an interconnected series of flat sacks called thylakoids that are grouped in stacks called grana
iii. the thylakoids enclose aqueous regions called the thylakoid lumen
iv. chlorophyll is found in the thylakoid membrane, and
the reactions of photosynthesis take place there and in
the stroma
v. carotenoids in the chloroplast serve as accessory
pigments for photosynthesis
E. endosymbiont theory
a. states that mitochondria and plastids evolved from
prokaryotic cells that took residence in larger cells and
eventually lost their independence
b. the cells containing the endosymbionts became dependent upon them for food processing, and in turn provide them with a protected and rich environment (a mutualistic relationship)
c. supporting evidence
i. the size scale is right-mitochondria and plastids are on
the high end of the size of typical bacteria
ii. endosymbionts also have their own DNA and their own
“cell” division; in many ways they act like bacterial
cells
iii. the DNA sequence and arrangement (circular
chromosomes) of endosymbionts is closer to that of
bacteria than to that found in the eukaryotic nucleus
iv. endosymbionts have their own ribosomes, which are
much like bacterial ribosomes
v. there are other known, more modern endosymbiotic
relationships: algae in corals, bacteria within
protozoans in termite guts
d. some genes appear to have been shuttled out of the
endosymbionts to the nucleus
e. many of the proteins used by endosymbionts are encoded by nuclear genes and translated in the cytoplasm (or on rough
ER) and transported to the endosymbionts
f. DNA sequencing of endosymbionts is being used to trace the evolutionary history of the endosymbionts
i. Appears that endosymbiosis began about 1.5 to 2
billion years ago (around when the first eukaryotic
cells appeared)
ii. Mitochondria appear to have a monophyletic origin
(one initial endosymbiotic event, giving rise to all
mitochondria in eukaryotic cells today)
iii. Plastids appear to have a polyphyletic origin (several
initial endosymbiotic events giving rise to different
plastid lines present today in algae and plants)
iv. Some argue that endosymbionts were simply derived
within the early eukaryotic cells, along with the
nuclear membrane and the proliferation of other
membrane surfaces common in eukaryotes but not
prokaryotes
X. Cytoskeleton
A. Eukaryotic cells typically have a size and shape that is maintained a. The cytoskeleton is a dense network of protein fibers that provides needed structural support
b. The network also has other functions
i. A scaffolding for organelles
ii. Cell movement and cell division (dynamic nature to the protein fibers is involved here)
iii. Transport of materials within the cell
B. The cytoskeleton is composed of three types of protein filaments: microtubules, microfilaments, and intermediate filaments C. Microtubules are the thickest filaments of the cytoskeleton a. Hollow, rod-shaped cylinders about 25 mm in diameter b. Made of α-tubulin and β-tubulin dimers
c. Dimers can be added or removed from either end (dynamic nature)
d. One end (plus end) adds dimers more rapidly than the minus end
e. Can be anchored, where an end is attached to something and can no longer add or lose dimers
f. Microtubule-organizing centers (MTOCs) serve as anchors i. Centrosome in animal cells
ii. Centrosome has two centrioles in a perpendicular
arrangement
iii. Centrioles have a 9x3 structure: 9 sets of 3 attached microtubules forming a hollow cylinder
iv. Centrioles are duplicated before cell division
v. Play an organizing role for microtubule spindles in cell division (other eukaryotes must use some alternative MTOC during cell division; still incompletely described) g. Microtubules are involved in moving organelles
i. Motor proteins (such as kinesin or dynein) attach to organelle and to microtubule
ii. Using ATP as an energy source, the motor proteins change shape and thus produce movement
iii. Microtubule essentially acts as a track for the motor protein
iv. Motor proteins are directional; kinesin moves toward the plus end, dynein away from it
h. Cilia and flagella are made of microtubules
i. Thin, flexible projections from cells
ii. Used in cell movement, or to move things along the cell surface
iii. Share the same basic structure; called cilia if short (2- 10 micrometer typically) and flagella if long (typically 200 micrometer)
iv. Central stalk covered by cell membrane extension, and anchored to a basal body
1. 9x3 structure
v. Stalk has two inner microtubules surrounded by nine
attached pairs of microtubules
1. 9+2 arrangement
2. Dynein attached to the outer pairs fastens the
pair to its neighboring pair
3. Dynein motor function causes relative sliding of
filaments; this produces bending movement of
the cilium or flagellum
vi. The basal body is very much like the centriole
1. Has a 9x3 structure
2. Replicates itself
D. Microfilaments are solid filaments about 7 nm in diameter
a. Composed of two entwined chains of actin monomers
b. Linker proteins cross-link the actin chains with each other and other actin associated proteins
c. Actin monomers can be added to lengthen the microfilament or removed to shorten it; this can be used to generate
movement
d. Important in muscle cells; in conjunction with myosin, they are responsible for muscle contraction
e. Also associate with myosin in many cells to form contractile structures, such as “pinching in” in cell division
E. Intermediate filaments
a. Typically, just a bit wider than microfilaments, this is the
catch-all group for cytoskeletal filaments composed of a
variety of other proteins
b. The types of proteins involved differ depending on cell types and on the organism; apparently limited to animal cells and
protozoans
c. Not easily disassembled, thus more permanent
d. A web of intermediate filaments reinforces cell shape and positions of organelles (they give structural stability)
e. Prominent in cells that withstand mechanical stress
f. Form the most insoluble part of the cell
XI. Outside the cell
A. Most prokaryotes have a cell wall, an outer envelope, and a capsule (capsule is also called glycocalyx or cell coat)
B. Most eukaryotic cells produce materials that are deposited outside the plasma membrane but that remain associated with it
a. Plants have thick, defined cell walls made primarily of cross linked cellulose fibers
i. Growing plant cells secrete a primary cell wall, which is
thin and flexible
ii. After a plant cell stops growing, the primary cell wall is
usually thickened and solidified, or a secondary cell
wall is produced between the primary cell wall and the
plasma membrane
iii. Secondary cell walls still contain cellulose, but typically
have other material as well that strengthens them
further (for example, lignin in wood)
b. Fungi typically have thinner cell walls than plants, made
primarily of cross-linked chitin fibers
c. Animals do not have cell walls, but their cells secrete varying amounts of compounds that can produce a glycocalyx and an
extracellular matrix (ECM)
Glycocalyx: polysaccharides attached
to proteins and lipids on the outer
surface of the plasma membrane
∙ Typically functions
in cell recognition
and
communication,
cell contracts, and
structural
reinforcement
∙ Often works
through direct
interaction with
ECM
ECM: a gel of carbohydrates and
fibrous proteins; several different
molecules can be involved
o Main structural protein is
tough, fibrous collagen
o Fibronectins are
glycoproteins in the ECM
that often bind to both
collagen and integrins
o Integrins are proteins in
the plasma membrane
that typically receive
signals from the ECM
Tour of the animal cell (video in class)
Phospholipids bilayer membrane in the cell
Purple blobs are protein involved in the space between cells
Cytoskeleton-structural framework of the cell that is made up of protein Sausage shape things are mitochondria; yellow dots are ATP
Nucleus (enclosed by a double membrane) and ribosomes
Blue -DNA; purple-protein that the DNA wraps around
Polar tops are in the cells, while the non-polar tails attached with each other Selective permeable
Facilitative diffusion (protein facilitator)