Chapter 1: The Science of Biology

Enumerate the properties of water that are important for life.

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  

What are the major types of organic molecules?

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. If you want to learn more check out What is spliceosome?

 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.

What are the characteristics of living matter?

 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 We also discuss several other topics like How should one approach topics in behavioral economics?

 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. Don't forget about the age old question of What is the definition of market segment?

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 study of matter?

∙ 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.

Hypothesis, theory, and law

∙ 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 Don't forget about the age old question of What is the cognitive model for?

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

∙ Science and technology-the goal of science is to understand nature; the goal  of technology is to apply scientific knowledge for a specific purpose We also discuss several other topics like What are the different types of earth crust?

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.

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)