Wednesday, September 16, 2009

Test 1 Study Guide

Hi, Everyone.

Here is the Study Guide for Test 1, which will be on Monday, 9/21/09. Following the Study Guide are my lecture notes for Chapters 1 - 3. The formating is a little off for the lecture notes, but it's still readable.

Test 1 Study Guide

Chapter 1

1. Know the cell theory.
2. Know the difference between a prokaryotic and eukaryotic cell.
3. Know the definition of the following terms: development, metabolism, adaption, genetics, homeostasis.
4. Know the various levels of biological organization, from atom to biosphere.
5. Know the definitions of the following: domain, kingdom, genera, species. Be able to place various organisms in the proper domain, kingdom, etc.
6. Know the source of genetic variation within a population.
7. Know the path of energy within an ecosystem. Know the definition of autotroph and heterotroph.
8. Know the definitions of hypothesis and theory. Know how to set up an experiment and the difference between a control and an experimental group.

Chapter 2

9. Know the definitions of the following: atom, proton, neutron, electron, element number, atomic number, atomic number, ion, cation, anion, isotope, polar covalent bond, non-polar covalent bond, ionic interactions, hydrogen bonding. Be able to apply the concepts listed above.
10. Know what determines the chemical behavior of an atom.
11. Be able to determine a mole or fraction of a mole of a molecule.
12. Know the parts of a chemical equation.
13. Know what a single, double, and triple covalent bond.
14. Know the characteristics of water that are important to life.
A. The mechanics of dissolving. The definitions of solvent, solute, and solution.
B. Specific heat, including the density of frozen water vs 4C water.
C. Adhesion, cohesion, and capillary action.
D. pH, including pH’s of various substances and the pH scale.
E. Know the buffers of human blood.

Chapter 3

15. Be able to identify single and double covalent bonds in a structural formula.
16. Know and be able to recognize the various isomers: structural, geometric, and enantimers.
17. Know the functional groups and their characteristics.
18. Know and be able to recognize condensation and hydrolytic reactions in all the four major groups.
19. Know what an amphipathic molecule is.
20. Know the various characteristics of carbohydrates.
A. Monosaccharids (trioses, pentoses, hexoses), disaccharids, and polysaccharids and examples of each.
B. Be able to recognize various carbohydrates.
21. Know the various characteristics of lipids.
A. Know the various classes of lipid: fatty acids, triacylglycerols, phospholipids, carotenoids, steroids.
B. Know the difference between saturated and unsatruated fats and their characteristics.
22. Know the various characteristics of proteins.
A. Be able to identify the characteristics of the side chains of amino acids, if they are hydrophobic, polar non-ionic, acidic, or basic.
B. Know the characteristics of primary, secondary, tertiary, and quaternary structures. Know what bonds hold each structure together.
C. Know the potential functions of proteins: motility, transport, protection, structure, energy storage, enzymes, regulation.
D. Know what denaturation is and what causes it.
23. Know the various characteristics of nucleic acids.
A. Know how the parts of a nucleotide.
B. Know how nucleic acids transfer information, from organism to organism or within the cell. Know the difference between DNA and RNA. Know the various forms of RNA.
C. Know how nucleic acids transfer energy. Know examples of energy transferring nucleotides.
D. Be able to recognize a nucleic acid/nucleotide.

Biol 1610
Chapter 1 Outline

I. Introduction
A. Introduce self
B. Cover safety issues
1. Exits
2. Emergency plan
a. Where to meet if need to exit the building
b. Make sure distance, 1.5 height of surrounding buildings.
c. If issues with exiting the building, get with me after, if want.
C. Pass out syllabus & course objectives
1. Course schedule
2. Quizzes and tests
a. Quizzes are worth ten points and handed out on Wednesday, due following Monday.
b. Normal tests are worth 100 points and are taken in class - if unable to, let me know and I will arrange for the test to be taken at the Sandy Testing Center.
c. If have special needs, let me know privately, if want.
d. Last day to get quizzes and tests in is the last day of class, April 23.
e. Final - comprehensive and worth 200 points, includes 15 department final questions.
3. Grading
a. Grading is on a straight points system.
b. Tests #2 & #3 are opportunities to raise your grade, if needed.
• Will know the questions ahead of time.
• Fig 8-4, pages 176 - 177, Fig 8-7, page 180 if want to start memorizing now.

4. Tips on passing the course
a. Having taken chemistry will help.

• Course is heavy on chemistry.
• If haven’t taken chemistry before, can pass if work hard.
• If haven’t taken chemistry before, will help when take chemistry later.

b. Read course objectives before reading chapter, so you know what points are important.
c. Read chapter before class - come ready with questions, points don’t understand.
d. Made sure understand the figures.
e. Memorize the bolded terms.
f. Study groups

• Explaining something to another person makes it clearer in your own mind.
• OK to work on quizzes as a group.

g. Use quizzes as study guides for tests.
h. Taking notes during lectures

• What I cover is important.
• If I write it on the board, it’s important.

i. Tutoring available at the Redwood Center.
II. Living vs Nonliving (Bacteria, Horse vs Rock)
A. Organisms are composed of cells
1. Introduce simplification in beginning classes - ‘we will lie to you occasionally.’ Use example of viruses
2. A cell is a unit of life - differentiates ‘outside’ from ‘inside.’
B. Organisms grow and develop
1. Rocks grow by sedimentation and igneous processes - radically different than started.
2. Bacteria and horses grow by metabolism - still approximately the same when started, with additions.
C. Organisms regulate their metabolic processes
1. Rocks degrade - oxidation, metamorphism
2. Bacteria & horses regulate growth and developement.
D. Organisms respond to stimuli
1. Rocks respond to gravity, erosion, etc.
2. Bacteria & horses respond to light, social, etc.
E. Organisms reproduce
1. A rock will produce gravel, gravel will produce sand.
2. Bacteria & horses produce other bacteria & horses, not kittens or puppies.
F. Populations evolve and become adapted to the environment.
1. A rock will ‘change’ but will not adapt.
2. Bacteria & horses
a. Bacterial antibiotic resistance
b. Different species of horses - donkeys, domestic horses, zebras
III. Hierarchy of Biological Organization (Fig. , page )
A. Reductionism vs Emergent properties
B. Chemical level
1. Human vs pond as far as water
C. Cellular level
1. Cells & organelles
D. Tissue
1. Osteocytes, bone marrow
E. Organ
1. Bone - strength, regity
F. Organ system
1. Skeletal system - strength, flexibility (joints)
G. Organism
1. Fully functional individual - movement, digestion, potential reproduction
H. Population
1. Social interaction, reproduction, change within
I. Community
1. Interaction between different populations - elephants eat one kind of browse, keep trees down
2. Zebras & wildebeests eat another type of browse, aid in watching for predators.
J. Ecosystem
1. Add geography and weather to community.
K. Biosphere
IV. Information Transfer Within Organisms
B. Chemical & Electrical signals
1. Nerve cells
2. Hormones
V. Systematics and Taxonomy
A. Systematics - field of biology that studies the diversity of organisms and their evolutionary relationships
B. Taxonomy - subspecialty of systematics, is the science of naming and classifying organisms.
C. Binomial system - Carolus Linnaeus, a Swedish botanist
Genus, specific epithet
D. Domain - species
VI. Domains & Kingdoms
A. Original - Animal & Plant Kingdoms
B. Animal, Plant, Microbes
C. Current - Microbiologist Carl Woese (woes) biochemistry of small subunit ribosomal RNA
1. Three Domains - Archaea, Bacteria, Eukarya
2. Eukarya is divided into Kingdoms Protista, Plantae, Animalia, Fungi
VII. Evolution by Natural Selection
A. Gene pool
1. Variation in the population - evolution in population, not individual
2. Bacterial drug resistance - evolution we can see because of short life span of bacteria
3. Galapogos finches - Darwin reasoned backwards
B. Selective pressures from their environment
1. Change - wide spread use of penicillin
2. Bulk of population killed
3. Those cells naturally resistant grow and take over population
VIII. Energy Cycles Within Ecosystems
A. Sun
B. Producers - plants mostly
C. Consumers - just about everything else
D. Decomposers - fungi & bacteria
9. Scientific Method
A. Systematic thought process
1. Deductive reasoning - begin with supplied information (premises) and draw conclusions from that information.
2. Inductive reasoning - specific observations and draw a conclusion or discover a governing principal.
B. Set up of an experiment
1. Hypothesis - beginning or end
2. Questions
3. Set up experiment to answer questions
4. Run experiment - limit variables (reductionist), set controls
5. Results either support or refute hypothesis - or, occasionally, give completely unexpected results - Flemming and penicillin
C. Theory
1. Supported by lots of supported hypothesis
2. Dynamic - paradigm shifts
Paradigm - set of assumptions or concepts that constitute a way of thinking about reality

Biol 1610
Chapter 2 Outline
Atoms and Molecules: The Chemical Basis of Life

I. Structure of the Atom
A. Subatomic Particles
1. Protons
a. Charge - positive
b. Mass - 1 amu (atomic mass units/dalton)
c. Location - nucleus of the atom
2. Neutrons
a. Charge - neutral
b. Mass - 1 amu
c. Location - nucleus of the atom
3. Electrons
a. Charge - negative
b. Mass - negligible
c. Location - orbit(s) outside the nucleus
4. Bohr models vs quantum mechanics - simplicity and usefulness in describing chemical reactions
a. Orbitals - used to describe how electrons move in 3-D
b. Electrons clouds - probabilities of where electrons are
c. Principal energy levels - electrons in orbitals with similar energies
d. Electron shells - further out, more energy
e. Valence electrons in valence shell - most energetic
f. Movement through shells by addition or loss of energy
B. Atomic Number of an Atom - number of protons
1. 6C Proton number below, atomic mass above
C. How Do Elements Differ From Each Other
1. Atomic number determines the characteristics of the element.
2. Different physical characteristics: gases vs liquids
3. Reactions with other elements
4. Will go over some of the different characteristics
D. Atomic Mass of an Atom
1. Protons plus neutrons
E. What Are Isotopes
1. Proton number is always the same for an element.
2. Neutron number may vary.
3. Atomic mass is unstable - radioactive.
Example of C-14: decays when neutron decays into a proton & β-particle to form N-14
F. What Are Ions?
Atoms with a charge.
II.. Periodic Table, Fig 2-1, page 27
A. How we organize elemental information
1. Chemical symbol
2. Atomic number
3. Chemical name
4. Atomic mass
5. Rows vs columns - valance shells vs valance electrons
B. Know names and symbols on the Table 2 - 1, page 26
B. Observe the location of these elements on the table Figure 2 - 1
C. Observe the electron configurations
1. Carbon vs Nitrogen
2. Nitrogen vs Phosphorous
III. Chemical Formulae
A. Molecules
1. Two or more atoms joined very strongly
2. Some elements naturally form molecules
a. Hydrogen & oxygen vs neon
B. Chemical compounds
1. Atoms of two or more different elements
a. Water - molecular
b. Salt - not molecular
C. Simplest
1. Expresses ratio
2. Not usually used in biology
D. Molecular
1. Expresses actual composition
2. Water - same as simplest
3. Hydrazine - NH2 vs N2H4
E. Structural
1. Expresses shape and bonds of the chemical
2. Useful in biology for showing reactions & structure
3. Polymers - molecular formula may not be as informative
a. Glucose - C6H12O6
b. Fructose - C6H12O6
IV. Avogadro’s Number
A. Molecular mass
1. Add up the atomic masses of the molecule
2. Water: (1 amu [H] x 2) + (16 amu [O] x 1) = 18 amu
3. Glucose: (12 amu [C] x 6) + (1 amu [H] x 12) + (16 amu [O] x 6) = 180 amu
B. What is a mole (mol)?
1. Amount of an element or compound whose mass in grams is equivalent to its atomic mass or molecular mass
a. 1 mol of water = 18 g
b. 1 mol of glucose = 180 g
2. A mol lets us make comparisons between atoms and molecules of different mass
3. 1 mol of any substance always has exactly the same number of units, no matter the size of the molecule
4. Avogadro’s number
a. 6.02 x 1023 - number of units (atoms or molecules) per mole
b. 1 mole of water is 18 g but contains 6.02 x 1023 molecules
c. 1 mole of glucose is 180 g but contains 6.02 x 1023 molecules
B. How is a mole of a chemical compound calculated?
1. Molecular mass then covert to grams

V. How to Write Chemical Reactions
A. Chemical equations describe chemical reactions
B. Reactants written on left, products on right, arrows indicate concentration at equilibrium
C. Glucose + oxygen 6carbon dioxide + water + energy
D. Carbon dioxide + water 6 carbonic acid
VI. Chemical Bonds
A. Covalent bond
1. A covalent bond is where the electron(s) are shared to fill valence shells
a. Water
b. Methane (CH4)
c. Ammonia (NH3)
2. Single vs double & triple
a. Singe bond - share one pair of electrons
b. Double bond - share two pairs of electrons
c. Triple bond - share three pairs of electrons
B. Ionic bond
1. Ions are atoms with a charge.
2. Electron striping
3. NaCl: Same valance shells (3) but Na has 1 valance electron, Cl has 7
4. Na+ Cl- - still associate through charge attraction
5. Dissolve in water
a. Solvent vs solute
b. Na attracted to O, Cl to H, separated
C. Redox reactions
1. Reduction - Oxidation reactions
“Leo goes ger”: lose an electron = oxidation, gain an electron = reduction
“Oil rig”: oxidation is losing, reduction is gaining
2. Reduction - donates electrons
3. Oxidation - accepts electrons
4. Oxidation of iron as an example
Draw reaction, then do Lewis structure with electrons leaving
4Fe + 3O2 6 2Fe2O3
D. Hydrogen bonds
1. What it is
a. Polar vs nonpolar covalent bond - electronegativity
• Water structure - oxygen ‘wants’ the electrons more, so the electrons ‘hang out’ around the oxygen nucleus more, giving it a slight negative charge.
• Water structure - hydrogen ‘wants’ the electrons less, so the electrons are further away, giving a slight positive charge.
• Water is then a polar molecule - one end negative and one end positive, like a magnet.
• Other covalently bonded molecules are equal in electronegativity - electrons hang out around the nuclei equally, so the molecule is nonpolar - no charge.
• Oils are an example of nonpolar molecules.

b. Attraction between polar hydrogen and a polar negative atom
c. Relatively weak - form and break often - together strong
2. What type(s) of molecules form hydrogen bonds?
a. Tend to form between an atom with a partial negative charge and a hydrogen bonded to oxygen and nitrogen
b. Water - the defining hydrogen bonding molecule.
c. Ammonia can form hydrogen bonds - important for protein structure.
3. How does hydrogen bonding affect the properties of water?
a. Cohesion - water molecules bond to self
1. Surface tension - greater attraction for self than air, pulled down attraction with molecules below
b. Adhesion - water molecules stick to other kinds of substances - charged groups
1. Wetting
2. Capillary action - combination of cohesion & adhesion to move against gravity
c. Hydrophilic vs hydrophobic
1. Dissolving sugar (polar) & salt (ionic)
2. Separation of oil (nonpolar) & water - water excludes oil
d. Water maintains a stable temperature
1. Boils at 100EC, 212EF, freezes at 0EC, 32EF
2. High heat of vaporization
a. amount of heat energy required to change 1 g of substance from liquid to vapor
b. hydrogen bonds resist separation into vapor
3. Evaporative cooling - As sample of water is heated, some move faster than others and enter evaporative state faster - take heat with them
4. Specific heat large - energy required to raise temperature of water - oceans and lakes are heat reservoirs - have constant temps & stabilize land temps
a. Deserts vs coasts
e. Floating of ice
1. Gas - widely separated
2. Liquid - hydrogen bonds form and break - molecules slip by each other
3. Solid - hydrogen bonds with four other adjacent molecules, regular crystalline lattice structure - lighter than liquid, more space between molecules
4. Why are the properties of water important to living things?
1. Universal solvent - hydrophillic
2. Hydrophobic - cell membranes
3. Capillary action - movement of water through soil
4. Stable temperature - constant temperature for life
5. Floating of ice - lakes & oceans don’t freeze completely

VII. Acids & Bases
A. Water dissociates slightly
1. HOH 6 H+ + OH- (or H3O+)
2. Same number of H+ (cations but called hydrogen ions) and OH- (anions but call hydroxide ions) ions, so pure water is neutral.
B. What is the difference between an acid & a base?
1. Acid - proton [H+] donor - hydrogen ions & anions
a. H Cl - hydrogen chloride dissociates to:
b. H+ : a proton/hydrogen ion
c. Cl- : an anion
2. Base - proton acceptor [OH-] - hydroxide ions & cations
a. NaOH - sodium hydroxide dissociates to:
b. Na+ : a cation
c. OH- : a hydroxide ion

d. NH3 + H2O - ammonia in water combine to form:
e. NH4+ :a cation formed by ammonia taking a H+ from water (ammionium ion)
f. OH- :an hydroxide ion from water
3. Salts - acid & base combined
1. H Cl + NaOH 6 NaCl + H2O
2. Hydrogen chloride donates an H+ and sodium hydroxide donates a OH-
3. H+ and OH- combine to form water.
4. Na+ (cation) and Cl- (anion) combine to form a salt (table salt)
5. A salt is the product of the combination of an strong acid and base.
6. Electrolytes

• Acids, bases, and salts in water dissociate to ions.
• Ions conduct electricity.
• Important in biology.

B. What is the scale which is used to measure the strength of acids and bases?
1. pH scale
a. Inverse log concentration of H+
b. Because inverse, the higher the concentration, the lower the pH.
2. Transparency of pH scale
3. Lower pH
a. More acidic
b. More H+ than OH- in solution or [H+] higher.
c. More H+ in solution, the stronger the acid or the reaction to dissociate will more completely proceed to the right.
4. Higher pH - more basic
a. More basic.
b. Less H+ than OH- in solution or [OH-] is higher.
c. More OH- in solution, the stronger the base or the reaction to dissociate will more completely proceed to the right.
C. What is a buffer?
1. Buffer is a substance or combination of substances that resist changes in pH when an acid or base is added
2. Buffering system includes a weak acid or a weak base
a. Do not ionize completely
b. At any given instant, only a fraction of the molecules are ionized - most are not dissociated
c. Carbonic acid in blood

• Carbonic acid is a weak acid - doesn’t completely dissociate like a strong acid (Hcl).
• More of the acid molecules keep the H+

CO2 + H2O 6 H2CO2 6 H+ + HCO3-
Carbon dioxide
Carbonic acid
Hydrogen ion
Bicarbonate ion

• Blood needs to remain with a narrow pH range, 7.4
• Too acid (too high [H+]) and will cause coma.
• Too alkaline (too high [OH-] and will cause convulsions.

d. Above reaction is at dynamic equilibrium

• Forward and reverse reactions are equal and relative components are not changing.
• Responds to stress (addition of hydrogen or hydroxide ions) by “shifting right” or “shifting left” to achieve a new dynamic equilibrium.
• Keeps pH ([H+]) stable.
• Add an acid/more H+ and will shift left to form more carbonic acid, effectively removing H+ ions from solution.

• Add a base/more OH- ions and OH ions will combine with H+ ions already in solution to form water, effectively removing OH- ions from solution.

Biol 1610
Chapter 3 Outline
Chemistry of Life: Organic Compounds

I. Organic Compounds
A. What is an organic compound?
1. Historically, a compound derived from life.
2. Found nonliving processes could create - chem lab.
3. New definition - carbon atoms covalently bonded to one another to form the backbone of a molecule.
4. Some very simple carbon compounds are considered inorganic because they are not bonded to another carbon or to hydrogen.
a. CO2 is considered inorganic.
• Produced by respiration - a life process.
• Produced by volcanism - a geologic process.
• Only one carbon without a hydrogen.

b. Methane (CH4) is considered organic.

• Metabolic by products of many organisms.
• Only one carbon but bonded to four hydrogens.
5. Most organic compounds are very large, macromolecules.

B. What is a hydrocarbon?
1. Consist of only hydrogen and carbon.
2. Review bonding properties of carbon
3. Structures
a. Chains Ethane & Butane
b. Double bonds: 1-Butene, 2-Butene
c. Branched chains: Isobutane
d. Rings: Cyclopentane, Benzene, Phenol
e. Joined rings & chains: Histidine
4. Single bonds - allow rotation around carbon - flexible
5. Double & triple bonds - inflexible, do not allow rotation
C. What is an isomer?
1. Structural isomers differ in the covalent arrangement of their atoms but have the same formula: C2H6O both ethanol and dimethyl ether
2. Geometric isomers are compounds that are identical in the arrangement oftheir covalent bounds but differ in the spatical arrangement of atoms or groups of atoms: trans-2-butene vs cis-2-butene
3. Enantiomers are isomers that are mirror images of each other but cannot be superimposed: models, D-glucose vs L-glucose
D. Why are isomers important is cells?
1. Structural isomers have different functions.
2. Enzymes recognize the difference between isomers, even down to enantiomers.
a. Cells produce one or the other
b. Trans-fatty acids vs cis-fatty acids
c. D vs L ‘sugars’
2. Biologically Functional Groups (Table 3 - 1)
A. Be able to recognize and/or depict the structural formulae for the seven functional groups listed.
1. ‘R’ represents the remainder of the molecule
a. ‘R’ is a bit like the root word in English.
b. ‘Use’ means one thing, but add ‘un’ and ‘d’, and you change the function.
c. In the same way, ‘R’ stands for the base molecule, in this case a hydrocarbon - add a functional group and the chemical behavior of the ‘root word’ or ‘remainder of the molecule’ of the changes.
d. Functional groups are like a prefix/suffix (‘un’ being the example) - always cause the same change in chemical behavior/meaning.
e. Continue analogy as we discuss functional groups.
2. Methyl groups (-CH3)
a. Common nonpolar functional group.
b. Hydrophobic
c. Used to turn genes on and off is one example of how it can change the function of an ‘R’ group.
d. Found in nearly every organic group.
e. Example, ethane (2 C gas) to propane (3 C gas)
3. Hydroxyl groups (-OH)
a. Remind about hydroxide ions.
b. Polar because electronegative O attracts covalent electrons.
c. Capable of H-bonding.
d. Hydrophilic
e. Found in alcohols.
f. Example, ethane (2 C gas) to ethanol (2 C liquid)
4. Carbonyl groups (C=O)
a. Aldehydes - on end of molecule, bonded to at least one H
b. Ketones - inside molecule, bonded to two other C
c. Polar because electronegative O attracts covalent electrons.
d. Hydrophilic
e. Found in
f. Example of aldehydes, formaldehyde ( O )
H - C - H
f. Example of ketones, propane (3 C gas) to acetone (3 C liquid)

5. Carboxyl (-COOH)
a. Weakly acidic because can release a H+
b. Can act as a buffer
c. Hydrophilic
d. Found in organic acids.
e. Example, ethane (2 C gas) to acetic acid/vinegar (2 C liquid)
e. Example, ethanol to acetic acid

f. Example, propane (3 C gas) to lactic acid (3 C liquid) [start cysteine]

6. Amino
a. Weakly basic, can accept an H+
b. Can act as a buffer.
c. Hydrophilic
d. Example, lactic acid with an amino group on C2 - amino acid (alanine)

7. Phosphate
a. Weakly acidic; one or two H+ can be released.
b. Used in energy transfer.
c. Found in nucleic acids, some lipips.
d. Example, phosphate ester found in ATP.

8. Sulfhydryl
a. Helps stablize internal structure of proteins by disulfide bridges/bonds.
b. Also called ‘thiols.’
c. Example, change alanine to cysteine by adding a sulfhydryl group to C1.

B. How does each of these affect the chemical properties of the organic compounds that contain them?
1. Methyl groups - hydrophobic functional group, nonpolar
2. Hydroxyl groups - hydrophilic functional group, polar
a. Ethanol (hydrophilic liquid [not as much as water]) vs ethane (hydrophobic gas)
3. Carbonyl groups - hydrophilic, polar
4. Carboxyl - carboxylic acids/organic acids, hydrophilic
a. Weak acids (reluctant to lose +H), exists as ionic & polar hydrophilic compound
5. Amino - weakly basic (accepts +H), hydrophilic ionic & polar
6. Phosphate - weakly acidic (lose 2 +H)
7. Sulfhydryl - sulfur bonds in proteins
3. Polymers
A. What is a polymer?
1. Macromolecules are giant molecules, consisting of thousands of atoms
2. Most macromolecules are polymers, produced by linking small organic compounds - monomers
3. Monomers are like letters in an alphabet - link them together to make different ‘words’ or compounds
B. Be able to describe the importance of hydrolysis reactions and condensation reactions in the breakdown and formation of polymers.
1. Hydrolysis - break down of polymers (to break with water)
2. Condensation - linking of monomers to form polymers
a. The equivalent of a water molecule is removed
b. Dehydration synthesis
3. Condensation reactions require energy
4. Hydrolysis & Condensation different process, require different enzymes, regulated separately

II. Four Major Large Organic Compounds
A. Carbohydrates
1. Characterize

a. Carbohydrate means “hydrate of carbon”, reflects the 2:1 ratio of hydrogen & oxygen, the same as in water
b. Carbon, hydrogen, and oxygen (CH2O)n ratio
c. Groups defined by structure.
d. Sugars, starches, and cellulose are examples of carbohydrates.
2. Include polymers?
Carbohydrates can be polymers.
3. Monomers used to form
a. Monosaccharide - one sugar unit
b. Disaccharide - two sugar units
c. Polysaccharide - many sugar units
B. Be familiar with some of the more common monosaccharides, disaccharides, and polysaccharides.
1. Figure 3-6, page 51 - Common monosaccharides
C. Describe how disaccharides and polysaccharides may be formed by condensation reactions between monosaccharides
Figure 3-7, page 53 - Condensation & hydrolysis
D. How may hydrolysis reactions be used to break glycosidic linkages.

E. What functions are associated with these molecules?
1. Monosaccharides - building blocks
2. Sugars & starches - energy, modification of other organic compounds
a. Fig 3-9, page 54.
b. α-glucose units goined by glycosidic bonds, combination of straight and branching chains.
3. Cellulose, chitin - structural
a. Fig 3-10, page 55
b. Structure of cellulose - composed of β-glucose units joined by glycosidic bonds to form a straight chain.

B. Lipids
1. Characterize
a. Heterogeneous group
b. Soluble in nonpolar solvents (ether & chloroform)
c. Relatively insoluble in water
d. Mainly carbon and hydrogen with few oxygen-containing functional groups
e. Biologically important groups: fats, phospolipids, carotenoids (yellow & orange plant pigments), steroids, and waxes.
2. Include polymers? Yes.
3. Monomers used to form
A. What is a fatty acid?
A long, unbranched hydrocarbon chain with a carboxyl group (-COOH) at one end
B. Be familiar with the major groups (and specific examples) of lipids
1. Triacylglyerols/triglycerides
a. A glycerol joined to three fatty acids
b. Glycerol - 3-C alcohol that contains 3 hydroxyl groups
c. Ester linkages - formation in a triacylglycerol Figure 3-12
d. How does a saturated fatty acid differ from an unsaturated fatty acid?
2. Phospholipids
a. Component of cell membranes
b. Member of group of lipids called amphipathic lipids - one end hydrophobic & other end hydrophilic
c. Structure of phospholipid (lecithin) Figure 3-13
d. How forms membranes - hydrophobic tails inside with each other, phosphate heads outside in water
3. Carotenoids
a. Pigments derived from isoprene units
b. Classified with lipids - insoluble in water, oily consistency
c. Isoprene to retinal Figure 3-14
4. Steroids
a. Contain four rings of carbon atoms
b. 3 rings contain 6 carbons, 4th contain five carbons
c. Cholesterol, bile salts, reproductive hormones, cortisol
d. Figure 3-15 Cholesterol & cortisol
e. Cholesterol found in cell membranes as well as running around doing damage in arteries. Also base for some hormones.
f. Cortisol base for hormones.

C. Proteins
1. Characterize
a. Macromolecules composed of amino acids
b. Most versatile cell components
2. Include polymers? Yes.
3. Monomers used to form - amino acids
A. What is a amino acid?
1. All have an amino group (NH2) and a carboxyl/acid group (COOH)
2. Because these two functional groups are the same in all amino acids, differences are in -R groups and other functional groups
3. Amino acids at pH 7 (body pH) exist mainly in their ionized form as dipolar ions. This becomes important in structure.
4. Nonpolar, polar/uncharged, acidic, basic - becomes important in structure & function (be familiar with Fig 3-16)
B. Protein structures
1. Primary
a. The amino acid sequence
b. Affected by peptide bonds
c. Basically a straight line
d. Show hook up of glycine & alanine, then cysteine

• Go over functional & R groups
• Go over condensation to form peptide bonds

2. Secondary
a. Results from hydrogen bonding involving the backbone - the double bonded O from one peptide bond can form H-bond with a N -H from another peptide bond
b. α-helix

• Forms a coil, 3.6 amino acids/turn - oxygen is part of the remnant of the amino group of the fourth amino acid down the chain
• R groups project out from sides
• Elastic - physical factors (shape - able to stretch and reform like a spring) and chemical factors (H-bonds easily broken and reformed
• Found in protein in hair, skin, wool, nails

c. β-pleated sheet

• Takes place between different polypeptide chains or different regions of a polypeptide chain that has turned back on itself - H-bonds hold neighboring strands together
• Fully extended chains zig-zag, so sheet is pleated
• Half R groups stick up and half stick down
• Strong & flexible but not elastic - distance between the pleats is fixed, determined by strong covalent bonds of the polypeptide backbones
• Found in cores of many globular proteins

3. Tertiary
a. Overall 3-D shape assumed by each individual polypeptide chain
b. Determined by 4 major factors that involve interactions among R groups/side chains

• Hydrogen bonds between R groups of certain amino acids subunits (threonine and serine)
• Ionic bonds between an R group with a positive charge (basic - lysine) and an R group with a negative charge (acidic - aspartic acid)
• Hydrophobic interactions result from the tendency of nonpolar R groups (glycine and alanine) to be excluded by the surrounding water and therefore to associate in the interior of the globular structure
• Covalent bonds known as disulfide bonds or disulfide bridges may link the sulfur atoms of two cysteine subunits belonging to the same chain. H’s removed and S covalently linked.
c. Figure 3-21 Expanded structure of a tertiary structure involving an α-helix. Tertiary structure involving α-helixes and β-pleated sheets. Structures stabilized by above 4 interactions

4. Quaternary
a. Interactions among peptides - not all proteins are composed of one polypeptide. Many proteins are associations of different peptides, or subunits, to form the functional protein.
b. Quaternary structure is the resulting 3-D structure.
c. Same type of bonds as secondary & tertiary structures

• H-bonding
• Ionic bonding
• Hydrophobic interactions
• Disulfide bonds
d. Antibodies - four polypeptide chains joined by disulfide bonds
Disulfide bonds stabilize secreted proteins
e. Hemoglobin - four polypeptide chains - two of each
f. Collagen - three polypeptide chains arranged in α-helixes coiled around each other and bound by cross-links between their amino acids
5. Amino acid sequence determines its conformation
a. Experiments in 1996 with myoglobin - self folding within microseconds in vitro
b. in vivo (inside cell) different from outside cell (in vitro)
Molecular chaperones
• Mediate folding of some protein molecules - more orderly & efficient
• Prevent partially folded proteins from becoming inappropriately aggregated
• No data to suggest actually dictate the folding pattern
6. Structure determines function
a. Domains - distinct structural region
b. Proteins may have more than one domain, each with different function
Enzyme -
• domain for grabbing the chemical to be modified
• domain for attachment of energy source
• domain for attachment to membrane
c. Sickle cell anemia
• Mutation causes substitution of valine (nonpolar) for glutamic acid (positive charged) at position 6 of the beta chain of hemoglobin
• Makes hemoglobin less soluble in water, wants to form crystal with self
• Changes red blood cells from donut shape/filled Life Saver to sickle shape
d. Cystic fibrosis also the case of a single amino acid mutation - mucous more sticky, doesn’t flow as well
e. Denaturation
• High ph, high heat, or certain chemicals will cause an amino acid to denature or unfold
• Results in a more random structure
• Results from disruption of hydrogen and ionic bonds
• Lose of function
• Some may return to original, functional structure, others do not - Fried egg example

C. What are some of the major functions carried out by proteins (Table 3 - 2, page 62)
1. Enzymes - catalyze specific chemical reactions - catalase
2. Structural proteins - collagen in joints (triple helix - stiff, α-helixes - elastic)
3. Storage proteins - ovalbumin in egg white, zein in corn kernels
4. Transport proteins - move nutrients from outside of the membrane to the inside
5. Regulatory proteins - hormones such as insulin.
6. Motile proteins - participate in cellular movements - myosin for muscle contractions
7. Protective proteins - defend against foreign invaders - antibodies, complement, etc.

D. Nucleic Acids
1. Characterize
2. Include polymers? Yes, joined by phosphodiester linkages
3. Monomers used to form - nucleotides
a. A five-carbon sugar, either deoxyribose or ribose
b. One or more phosphate groups that make the molecule acidic
c. A nitrogenous base - a ring compound that contains nitrogen
4. Purines & Pyrimidines
a. Purines - two joined carbon chains, can form two H-bonds
b. Pyrimidines - one carbon chain, can form three H-bonds
5. Polynucleotides

• Linear chains of nucleotides joined by phosphodiester linkages, each consisting of a phosphate group and the covalent bonds that attach it to the sugars of adjacent nucleotides
• Nucleotides defined by base
• Joined in any order - code like a 4 letter alphabet

5. RNA
a. Composition

• A ribose sugar base
• A - adenine, purine
• G - guanine, purine
• C - cytosine, pyrimidine
• U - uracil, pyrimidine
• Usually composed of one nucleotide chain - ribose bases joined by phosphodiester linkages, nucleotides ‘stick out’

b. Functions

• Transport of information from the nucleus - mRNA
• Enzymatic functions - rRNA
• Transport of amino acids to where they will be formed into polypeptides - tRNA

6. DNA
a. Composition

• A deoxyribose base
• A - adenine, purine
• G - guanine, purine
• C - cytosine, pyrimidine
• T - thymine, pyrimidine
• Usually composed of two nucleotide chains (deoxyribose bases joined by phosphodiester linkages, nucleotides ‘stick out’) held together by hydrogen bonds and intertwined - double helix

b. Functions

• Storage of genetic information - stable macromolecule
• Transmission of genetic information - because of double helix, can be duplicated ‘exactly’
• Expression of genetic information - translation into mRNA, gene regulation

7. Be familiar with the biologically important nucleotides
a. ATP

• adenosine triphosphate - adenine, ribose, three phosphates
• Figure 7-5 Structure
• Two terminal phosphate groups - covalent bonds
• Can donate energy through transfer of a phosphate group - most of the cells energy

b. GTP

• guanosine triphosphate - guanine, ribose, three phosphates
• Like ATP
• Energy and cell signaling

c. Dinucleotide NADH.

• nicotinamide adenine dinucleotide
• Primary role in oxidation and reduction reactions in cells
• NAD+ or NADH (accepted electrons)

E. Summary (Table 3 - 3, page 69)

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