Biology 101 Chapter 2

Small Molecules: Structure and Behavior


1.  Distinguish between the terms atom and element and describe the structure of an atom.

---atom is the smallest unit of a chemical element

   --consists of a nucleus and one or more electrons

---element is a pure substance that contains only one type    of atom

---atom consists of dense, positively charged nucleus around which

   one or more negatively charged electrons move

---nucleus contains one or more positively charged particles (protons)

   and may also contain neutral charged particles (neutrons)

---atoms and their components have mass

   --mass measures the quantity of matter present

2.  State the six elements essential to life that make up 98% of living matter.

---C, H, N, O, P, and S

3.  Define and distinguish among atomic number, mass number, atomic weight, and valance.

---an element is distinguished from other elements by the number of

   protons (in the nucleus)in each of its atoms

---this number, which does NOT change, is called the atomic number

   of the element

---every element (except hydrogen) has one or more neutrons  in its


---mass number of an atom equals the total number of protons and

   neutrons in the nucleus

---atomic mass (atomic weight) is the average of the mass numbers

   of a representative sample of atoms of the element, with all

   isotopes in their normally occurring proportions

---valence describes the bonding capacity of an atom and is generally

   equal to the number of unpaired electrons in the atom’s outermost


   --valence electron = electrons in outermost electron shell

   --valence shell = outermost energy shell of an atom containing

     the valence electrons involved in the chemical reactions of

     the atom

4.  Explain why radioisotopes are important to biologists.

---isotopes of the same element have same number of protons, but

   differ in the number of neutrons in the nucleus

---12C; 13C; 14C

---radioisotopes are unstable and give off energy as α (alpha),

   β (beta); or γ (gamma) radiation from the nucleus

---such decay transforms the original atom into another atom (usually

   of another element)

---used in medicine (radiation therapy) and in science in radioactive

   dating and other experiments

5.  Describe the location of electrons and explain how electron behavior influences the chemical behavior of an atom.

---region of space where electron is found 90% of time is the

   electron’s orbital

---in an atom, a given orbital can be occupied by at most TWO electrons

---orbitals constitute a series of electron shells (energy levels)

---first (innermost) energy shell consists of only ONE orbital so can

   only hold two electrons

---second shell made up of FOUR orbitals = maximum of 8 electrons

   --1 s and 3 p orbitals

---for our course, 1st shell = 2; 2nd shell = 8; 3rd shell = 8

---atoms of chemically reactive elements seek to attain the stable

   condition of having NO unpaired electrons in their outer shells

---this stability is attained by sharing electrons with other atoms,

   or by gaining or losing one or more electrons from outermost shell

---molecule is defined as two or more atoms linked by chemical bonds

---tendency of atoms in stable molecules to have eight electrons in

   their outermost orbit is known as the octet rule

6.  Distinguish among nonpolar covalent, polar covalent, and ionic bonds.

---covalent bond occurs when two atoms attain stable electron numbers

   in their outer shells by sharing one or more pairs of electrons

---good example is hydrogen

---covalent bonds are quite strong and stable

---single unbroken line represents a PAIR OF SHARED ELECTRONS

---electronegativity is the attractive force that an atom exerts on


   --determined by # of protons and how far away the electrons are from

      the nucleus

---**closer two atoms are in electronegativity, the more EQUAL their

   sharing of electrons will be

---when electrons are shared equally (more or less), the bond is called

   nonpolar covalent

---when atoms with differing electronegativity valves share electrons,

   the more electronegative atom is “electron greedy”

   --“will bond but I get to keep them more than you”

---unequal sharing of electrons in a covalent bond is called a

   polar covalent bond

---unequal sharing results in a slightly negative charge associated

   with more electronegative atom and a slightly positive charge on

   the less electronegative atom

   --δ- and δ+

---bond is polar because these opposite charges are separated at the two

   ends of the bond

---partial charges that result from polar covalent bonds produce polar

   molecules or polar regions of large molecules

   --polar bonds greatly influence the interactions between molecules

      that contain them

---an ION is an atom that has lost or gained an electron or electrons

---when one interacting atom is much more electronegative than the other,

   a complete transfer of one or more electrons may occur

---chalk talk time with sodium and chlorine

---some elements form ions with multiple charges by losing or gaining

   more than one electron

   --Ca2+; Fe3+

---groups of covalently bonded atoms that carry an electric charge are

   called complex ions (NH4+; SO  ; and PO  )

---ionic bonds are bonds formed by electrical attractions between ions

   bearing opposite charge

---ions with one or more units of charge can interact with polar

   molecules as well as with other ions

   --dissolve salt in water

7.  Name the two types of ions and describe how ionic bonds form between positive and negative ions.

---atom that loses an electron (or electrons) becomes positive ion

---atom that gains an electron (or electrons ) becomes negative ion

---opposite charges attract each other

---ionic bond formed by electrical attraction between ions with

   opposite charges

   --NaCL; CaCl2

---in solids, ionic bonds are strong because ions are close together

---in water (solvents), ionic bond much weaker

---hydrophilic versus hydrophobic

8.  Describe the formation of a hydrogen bond and describe the conditions under which a hydrogen bond will form.

---hydrogen bond may form between an electronegative atom and a

   hydrogen covalently bonded to a different electronegative atom

---also form between water molecules because water is polar molecule

   --many properties of water dependent on hydrogen bonding

---is very weak bond, but because of large numbers, they can influence

   the structure and properties of substances

9.  Explain what happens in a chemical reaction.

---chemical reaction occurs when atoms combine or change bonding


---reactants and product(s)

---matter cannot be created nor destroyed

---energy is the capacity to do work but can be thought of as the

   capacity for change

---chemical reactions do NOT create or destroy energy, but CHANGES

   in energy usually accompany chemical reactions

10. Explain how water’s polarity allows it to form hydrogen bonds amongst other water molecules.

---in liquid water, the negatively charged oxygen atom of one water

   molecule is attracted to the positively charged hydrogen atoms of

   another water molecule

   --water is a polar molecule

---shape of water molecule (tetrahedron), its polar nature, and its

   capacity to form hydrogen bonds give water its unusual properties

---ice floats, water is an excellent solvent making it ideal medium

   for biochemical reactions, water is both cohesive (sticking to

   itself) and adhesive (sticking to other things) and energy

   changes that accompany its transitions from ice-->liquid-->gas

   are important in living systems

11. List the five unique structural and special properties of water that make it an excellent for life.

---ice floats

   --solid water is LESS dense than liquid water

---melting and freezing

   --takes great deal of heat energy to melt ice

   --great deal of heat must be lost from water to change from liquid

      to solid

   --these properties make water a moderator of temperature change

---heating and cooling

   --liquid water has a high heat capacity

   --specific heat of substance is amount of heat energy required to

      raise 1 gram of substance by 10C

   --takes relatively large amount of heat just to break hydrogen bonds

     that hold liquid together

---evaporation and cooling

   --water has high heat of vaporization

   --requires a lot of heat to change from liquid to a gas

   --this heat is absorbed from environment in contact with the water

   --evaporation has cooling effect on the environment

   --explains why sweating cools the human body

   --as sweat evaporates from skin, it uses up some of the adjacent

     body heat

---cohesion and surface tension

   --cohesive strength of water permits narrow columns of water to stretch

     from roots to leaves of trees (> 100 m)

     -water evaporates from leaves (transpiration) = pull of water

   --water has high surface tension which means that surface of

      liquid water exposed to air is difficult to puncture

12. Describe the components of a solution.

---a solution is produced when a substance is dissolved in water

   (aqueous solution) or another liquid

---solution composed of solvent (what’s doing the dissolving) and

   a solute(s) (substance(s) being dissolved)

---qualitative analysis deals with substances dissolved in a solvent

   and the chemical reactions that occur there

---concentrations = amount of substance in a given amount of solution

13. Define molarity and list some advantages of measuring substances in moles.

---mole is amount of ion or compound in grams whose weight is

   numerically equal to its molecular weight (one mole of sugar

   weighs 342 g)

---chemists use a constant that relates the weight of any substance

   to the number of molecules of that substance

---Avogadro’s number = 6.02 x 1023 molecules per mole

---1 mole of substance dissolved in water to make 1 liter is called

   a 1 molar (1M) solution

---many molecules present in living systems exist in micromolar (uM)

   to millimolar (mM) [ ]s

---a 1 uM solution has 6.02 x 1017 molecules of the solute per liter

14. Define acid and base and explain how they change the hydrogen ion concentration.

---an acid releases H+ ions (protons) in solution

---a base accept H+ ions

---there are strong acids and bases and weak acids and bases

---terms “acidic” and “basic” refer only to solutions

---how acidic or basic a solution is depends on the relative [ ]s

   of H+ and OH- ions in it

---“acid” and “base” refer to compounds and ions

   --compound or ion that is an acid will donate H+

   --one that will accept a H+ is a base

15. Demonstrate how water dissociates using the equation for the dissociation of water.

---water molecule has slight but significant tendency to ionize into

   a hydroxide ion (OH-) and a hydrogen ion (H+)

---2 water molecules participate in the ionization

---one of the 2 “captures” a hydrogen ion (H+) from the other

   --forms a hydroxide ion (OH-) and hydronium ion (H30+)

---for simplicity: H2O---> H+ + OH-

---ionization of water is very important for all living creatures

16. Explain the basis of the pH scale.

---pH stands for “potential of Hydrogen”

---pH value defined as the negative logarithm of the hydrogen ion

   concentration in moles per liter (molar concentration)

---pH = -log10[H+]

---in practical terms, a lower pH means a higher H+ [ ] or greater


---water is neutral at pH 7

---solutions with pH of less than 7 are acidic

---solutions with pH greater than 7 are basic

---**pH scale is logarithmic

17. Use the bicarbonate buffer system to explain how a buffer functions to maintain the pH of a solution relatively constant.

---buffers are chemical systems that maintain relatively constant pH even

   when substantial amounts of acid or base are added

---a buffer is a mixture of a weak acid and its corresponding base

   --good example is carbonic acid (H2CO3) and bicarbonate ions (HCO3-)

---acid added to this solution, some H+’s will combine with bicarbonate

   ions to make carbonic acid

   --this uses up some of the H+’s in the solution and decreases the

      acidifying effect of the added acid

---base added to solution, carbonic acid ionizes to produce bicarbonate ions

   and more H+’s which counteract some of the added base

---buffer minimizes the effect of an added acid or base on pH

---given amount of acid or base causes a smaller change in pH in a

   buffered solution than in unbuffered solution

---essentially reversible reactions (chalk talk time again)

---law of mass action states that addition of component on one side

   of reversible reaction drives the reaction in direction that uses up

   that compound

18. Define organic.

---organic is defined as containing carbon atoms

   --what does one do with CO2?

---we shall define an organic molecule as one that contains both

   carbon and hydrogen

19. Functional groups impart special properties to molecules.  Recognize the major functional groups found on organic molecules.

---chemists use characteristics of composition, structure, reactivity,

   and solubility to distinguish a sample of one pure molecule from


---functional groups are groups of atoms that make up part of larger

   molecule and have particular chemical properties

   --shape, polarity, reactivity, and solubility

---hydroxyl, carbonyl (aldehyde, ketone), carboxyl, amino, phosphate,




Added objective

20. Define isomer and differentiate between structural and optical isomers.

---isomers are molecules that have the same chemical formula but

   different arrangements of the atoms

---structural isomer differ in how their molecules are arranged

---optical isomers are mirror images of each other

   --amino acids and many sugars

   --D-amino acids and L-amino acids

   --dextro and levo

   --only L-amino acids are commonly found in most organisms


Biology 101 Chapter 2

Student Self Assessment Short Answer


1.  Every atom except ______________ has one or more neutrons in its nucleus.


2.  The nutritionist’s Calorie, which biologists call a kilcalorie, is the equivalent of __________ heat-energy calories.


3.  The chemical properties of an element are determined by the number of _________ its atoms contain.


4.  The attraction between a slight positive charge on a hydrogen atom and the slight negative charge on a nearby atom is a(n) _____________________  _______________.


5. A chemical reaction that can proceed in either direction is called a __________________  ________________________.


6.  A ________________ is two or more atoms linked by chemical bonds.


7.  A ____________ is the amount of heat needed to raise the temperature of 1g of pure water from 14.5o C to 15.5o C.


8.  The sum of the atomic weights in any given molecule is called its ____________________  ________________________.


9.  ________________  __________________ occurs when one atom, such as 14C, is transformed into another atom, such as 14N, with an accompanying emission of energy.


10. The water strider skates along the surface water due to a property of liquids called _____________  ______________.



Biology 101 Chapter 2

Student Self Assessment Multiple Choice

____1.  Because atoms can have different number of neutrons, elements have ________.

      a. isotopes                b. more than one atomic number

      c. more than one atomic mass  d. both b and c


____2.  The atomic number of an element is the same as the number of ____.

      a. neutrons in each atom      b. protons plus electrons in each atom

      c. protons in each atom         d. neutrons plus protons in each atom


____3.  The mass number of an element is the same as the number of _____.

      a. electrons in each atom      b. protons in each atom

      c. neutrons in each atom      d. protons plus neutrons in each atom


____4.  What determines is a molecule is polar, nonpolar, or ionic?

      a. number of protons           b. bond distances

`     c. differences in electronegativities of the atoms

      d. the ionic charges


____5.  A single covalent chemical bond represents the sharing of how many electrons?

      a. one                        b. two

      c. three                   d. four


____6.  Which contains more molecules, a mole of hydrogen or a mole of carbon?

      a. a mole of carbon            b. a mole of hydrogen

      c. both contain the same number of molecules

      d. it depends on the pressure


_____7.  Specific heat is defined as ______.

      a. the heat released from ice during freezing

      b. the heat needed to raise the temperature of water

      c. one calorie

      d. the calories needed to raise a gram 1oC


____8.  An alkaline solution contains _____.

      a. more OH- ions than H+ ions

      b. more H+ ions than OH- ions

      c. the same number of OH- ions and H+ ions

      d. no OH- ions


_____9.  What is the difference between an acid and a base?

      a. An acid undergoes a reversible reaction, while a base does not.

      b. An acid releases OH- ions in solution, while a base accepts

         OH- ions.

      c. An acid releases OH- ions in solution, while a base releases

         H+ ions.

      d. An acid releases H+ ions in solution, while a base accepts H+ ions.


____9. Which of the following is the correct order for the relative strengths of chemical bonds?

      a. covalent, ionic, hydrogen, van der Waal forces

      b. ionic, covalent, hydrogen, van der Waal forces

      c. van der Waal forces, covalent, ionic, hydrogen

      d. hydrogen, covalent, van der Waal forces, ionic

Biology 101 Chapter 3

Macromolecules: Their Chemistry and Biology


1.  Explain how carbon’s electron configuration determines the kinds and numbers of bond carbon will form.

---carbon has 4 valence electrons in second energy level (shell)

   --would like to have that level filled

   --takes four electron gain or loss to do that

   --difficult to “steal” or “have stolen” four electrons

---best strategy is to “share” electrons

---carbon readily forms four COVALENT bonds with other carbon

   atoms or other atoms

---chalk talk time

2.  Describe a condensation and hydrolysis reaction in your own words.

---condensation reaction also called “dehydration synthesis”

   --both terms refer to the loss of water

   --results in covalently bonded monomers = polymers

   --polymers will form only if energy is added to system

   --reaction produces water molecules

---hydrolysis reaction is the reverse of condensation reaction

   --will digest polymers and produce monomers

   --reaction requires water

   --elements “H” and “O” of water become part of the products

   --also require the addition of energy

---KEY is to look for the water

   --if water is to left of arrow = hydrolysis reaction

   --if water is to right of arrow = condensation reaction

3.  List the four major groups of organic macromolecules.

---carbohydrates; proteins; lipids, and nucleic acids

4.  Name the monomer and polymer form of each organic biomolecule.

---carbohydrates-->monosaccharide; disaccharides;

   oligosaccharides; and polysaccharides

---proteins-->amino acids (20 common to living organisms)

---lipids-->simple lipids (triglycerides); phospholipids;

   carotenoids; steroids; waxes; vitamins (A, D, E, K)

---nucleic acids-->nucleotides

   --DNA and RNA

   --five carbon sugar; one of four nitrogenous bases, and a

     phosphate group

5.  Describe the distinguishing features of a protein and provide some functions for proteins.

---composed of monomers of amino acids (20)

---each protein has characteristic amino acid composition

   --not every protein contains all kinds of amino acids nor

     an equal number of different ones

---in some cases, prosthetic groups may be attached covalently

   to the protein

   --carbohydrates, lipids, phosphate groups, heme group, and

      metal ions such as copper and zinc

---amino acids may have charged side chains, polar but uncharged

   side chains, hydrophobic side chains, and three “special


---structural support, protection, catalysis (enzymes),

   transport, defense, regulation, and movement

---proteins normally not involved in energy storage and heredity

6.  Name the functional groups of an amino acid and describe how amino acids are bonded to create a protein.

---each amino acid has four different groups attached to central

   (a) carbon

   --a hydrogen, an amino group (NH3+), a carboxyl group (COO-),

     and a side chain (R group)

---carboxyl group of one amino acid reacts with amino group of

   another-->condensation reaction-->forms peptide bond

---N terminus--->C terminus

---polar covalent bonds important to polypeptide structure/shape

7.  Distinguish between primary, secondary, tertiary, and quaternary structure of a protein.

---primary structure is the sequence of amino acids

   --peptide backbone consists of repeating sequence of NCC-NCC

---precise sequence of AAs determine how the protein can twist

   and fold

   --adopts specific stable structure that distinguishes it from

     every other protein

---secondary structure consists of regular, repeated patterns

   in different regions of polypeptide chain

   --a helix and b pleated sheet

---a helix is right-handed coil threaded in same direction as

   standard wood screw

---coiling results from hydrogen bonds between hydrogen of amino

   group and C=O of another

---evident in insoluble fibrous structural proteins called

   keratins (hair, hooves, and feathers)

---b pleated sheet formed from 2 or more polypeptide chains

   almost completely extended and very close to each other

   --stabilized by H bonds between N-H on one chain and C=O

     groups on the other

   --spider silk or between different regions of same PP bent

     back on itself

---tertiary structure results when PP chain is bent at specific

   sites and folded back and forth

---reactions between R groups determine tertiary structure


---covalent disulfide bridges can form between specific cysteine


---hydrophobic side chains aggregate together in interior of


---Van der Waals forces stabilize close interactions between

   hydrophobic residues

---ionic interactions can occur between + and – charged side

   chains buried deep within protein, away from water, forming

   salt bridge

---both secondary and tertiary structure derive from protein’s

   primary structure

---quaternary structure results from ways multiple PP subunits

   bind together and interact

   --hydrophobic interactions, van der Waals forces, hydrogen

     bonds, and ionic bonds all help hold subunits together

   --hemoglobin (four folded PPs, 2 a and 2 b subunits)

8.  Explain how the structure of a protein relates to its function.

---specific shapes of proteins allow them to bind noncovalently

   with other molecules which in turn allows other important

   biological events to occur

   --cells stick together; carrier proteins; enzyme function;

     multi-protein DNA polymerase; multi-protein ribosome;

     receptor protein; defensive proteins (antibodies)

---biological specificity depends on shape of protein AND

   surface groups that it presents to a substance (ligand)

   attempting to bind to it

   --groups on surface are the R groups of exposed amino acids

     and are property of its primary structure

---three-dimensional structure of protein determines what it

   binds and therefore ITS FUNCTION

---shape determined by weak forces and is SENSITIVE to

   environmental conditions that upset weaker noncovalent


---elevated temperatures, pH changes, altered salt [ ]s

   can cause protein to adopt different shape/structure

---loss of normal tertiary structure called DENATURATION and

   is always accompanied by loss of normal biological function

---may or may not be reversible

---are 2 occasions when PP chain in danger of binding the wrong


   --following denaturation

   --just been synthesized and has not yet folded completely

---chaperonins (proteins) designed to limit inappropriate

   protein interactions

   --some work by trapping proteins inside molecular “cage”

   --may be “heat-shock” proteins

9.  Describe the distinguishing features of carbohydrates and differentiate between the categories of carbohydrates.

---diverse group of compounds containing carbon atoms flanked

   by hydrogen and hydroxyl groups (H-C-OH)

---mono; di, oligo (3-20); and polysaccharides

---monosaccharide ratio is 1:2:1

---others differ because of loss of 2 H’s and 1 O per each

   condensation reaction

10. Provide functions for carbohydrates in general and specifically for polysaccharides.

---have two major biological roles

   --source of energy and as carbon skeletons that can be

     rearranged to form other important molecules for

     biological structures and functions

---glucose fuel of choice for most living entities

   --exists as straight chain or ring

   --a and b ring forms which differ only in placement of H

     and OH attached to carbon 1

   --chalk talk time on numbering of carbons in ring

---ISOMERS have same chemical formula but different structural


   --C6H12O6 = glucose, fructose, mannose, and galactose

     -called “hexoses”

---pentoses are 5-carbon sugars

   --ribose and deoxyribose

   --some pentoses found primarily in cell walls of plants

---monosaccharides covalently bonded together by condensation

   reactions that form glycosidic linkages

---mono + mono = disaccharide

   --sucrose (glucose + fructose); lactose (glucose + galactose)

     maltose (glucose + glucose)

---oligosaccharides contain several monosaccharides linked by

   glycosidic linkages at various sites

   --many have additional functional groups which give them

     special properties

   --often covalently bonded to proteins/lipids


   --serve as cell recognition signals

   --ABO blood groups get their specificity from oligosaccharide


---polysaccharides are giant chains of monosaccharides

   --starch (glucose with a orientation)

   --cellulose (glucose with b linkages)

     -found in cell walls of plants; most abundant organic

      compound on Earth

---starches distinguished by amount of branching

   --amylose (plant starch) not highly branched

   --glycogen (animal starch) is highly branched

---1000 glucose molecules compared to one glycogen molecule and

   osmotic pressure

---some carbos modified by adding functional groups such as

   a phosphate and amino groups

---when amino group is substituted for an –OH group, amino

   sugars are formed

   --glucosamine and galactosamine

     -important in extracellular matrix

     -galactosamine major component of cartilage

     -glucosamine derivative produces chitin

11. Describe the characteristics that differentiate nucleic acids from other organic macromolecules and provide functions for nucleic acids.

---nucleic acids are polymers composed of monomers of


---two types of nucleic acids

   --deoxyribonucleic acid and ribonucleic acid

---DNA molecules are giant polymers that encode hereditary info

   and pass it from one generation to generation

---RNA molecules of various types copy info in DNA to allow

   construction of proteins

---DNA contains the info and RNA does the work

12. List the three components of a nucleotide.

---five carbon sugar (pentose); one of four nitrogenous bases;

   and a phosphate group

---DNA contains deoxyribose sugar; adenine, cytosine, guanine,

   and thymine

---RNA contains ribose sugar; adenine, cytosine, guanine, and


---molecules of pentose sugar and nitrogenous base but NO

   phosphate group are called nucleosides

---double ringed nitrogenous base called a purine

---single ringed nitrogenous base called a pyrimidine

13. Describe the properties of lipids that distinguish them from other organic macromolecules.

---lipids are diverse group of hydrocarbons

---composed of lots of C’s and H’s

---property they all share is insolubility in water

   --strongly hydrophobic

   --due to presence of many nonpolar covalent bonds

---not polymers in strict chemical sense since their units

   (lipid molecules) not held together by covalent bonds

   --weak, but additive van der Waals forces hold them together

---can be considered polymers of individual lipid units



---fats and oils (store energy); phospholipids (structural roles

   in cell membranes); carotenoids (help plants capture energy);

   steroids and modified fatty acids (regulatory roles as

   vitamins and hormones); thermal insulation; lipid coating

   around nerves (insulation); oil or wax (on skin, fur, and

   feathers repel water)

14. Name and describe the three types of lipids.

---fats and oils store energy

---also called triglycerides (simple lipids)

---building blocks are glycerol and fatty acids

---carboxyl group of fatty acid reacts with hydroxyl group of

   glycerol to form an ester

   --reaction product of an acid and an alcohol (+ water)

---phospholipids are important structural part of membranes

   --glycerol, two fatty acids, and phosphate group

   --part hydrophilic and part hydrophobic

   --chalk talk time again

   --“bilayer of phospholipids”

---carotenoids and steroids

   --carotenoids are family of light-absorbing pigments found

     in plants and animals

   --b-carotene can be broken down into 2 vitamin A molecules

     -rhodopsin formed from Vitamin A (needed for vision)

---responsible for color of carrots, tomatoes, pumpkins, egg

   yolks, and butter

---steroids composed of multiple rings sharing carbon atoms

   --three 6 carbon rings and one 5 carbon ring

   --cholesterol important constituent of membranes

   --testosterone and estrogens are hormones

   --cortisol (& others) important in regulatory roles in

     digestion of carbos and proteins, maintenance of salt and

     water balance, and in sexual development

---some lipids are vitamins (A, D, E, and K)

---some are waxes and oils for waterproofing

   --wax composed of fatty acid + long alcohol

15. Distinguish between a saturated and unsaturated fat and list some properties of each type of fat.

---saturated fatty acids contains NO double bonds

   --all bonds saturated with hydrogens

   --relatively straight and rigid

   --pack together tightly

---unsaturated fatty acids contain one or more double bonds

   --causes kink in molecule

   --prevent them from packing together tightly

---animal triglycerides versus plant triglycerides


Biology 101 Chapter 3

Student Self Assessment Short Answer


1.  Many monosaccharides like fructose, mannose, and galactose have the same chemical formula as glucose (C6H12O6), but the atoms are combined differently to yield different structural arrangements.  These varying forms of the same chemical formula are called _____________________.


2.  The highly branched polysaccharide that stores glucose in the muscle and the liver of animals is ________________.


3.  In proteins, amino acids are linked together by _________________ bonds.


4.  The linear arrangement of amino acids in the polypeptide chain is referred to as the ___________________

structure of the protein.


5.  Starch is a polymer of glucose subunits.  The subunits of any polymer are called _____________________.


6.  Fatty acids with more than one carbon-carbon double bond are called __________________________________.


7.  Cholesterol, vitamin D, and testosterone all have a multiple-ring structure and are members of a family of lipids known as ____________________________.


8.  Carbohydrates made up of two simple sugars are called ______________________________.


9.  All amino acids have a hydrogen atom, a carboxyl group, and an amino group attached to a carbon atom.  The variability in the 20 different amino acids lies in the structure of their ________  ______________________.


10.  The reaction A—H + B—OH --> A—B + H2O represents a _________________________  _____________________________. 

Biology 101 Chapter 3

Student Self Assessment Multiple Choice


____1.  The major classes of biologically significant large molecules include the _______________.

     a. proteins                   b. nucleic acids

     c. carbohydrates                  d. lipids

     e. all of the above


____2.  One has isolated an unidentified liquid from a sample of beans.  The liquid is added to a beaker of water and shaken vigorously.  After a few minutes, the water and the other liquid separate into two layers.  To which class of biological molecules does the unknown liquid most likely belong?

     a. carbohydrates                  b. lipids

     c. proteins                   d. nucleic acids


____3.  The portion of a phospholipid that contains the phosphorus group has one or more electric charges.  That makes this region of the molecule _______.

     a. hydrophobic                    b. hydrophilic

     c. nonpolar                   d. unsaturated


____4.  The monomers that make up polymeric carbohydrates like starch are called _______.

     a. nucleotides                    b. trisaccharides

     c. monosaccharides           d. nucelosides


____5.  A nucleotide contains a pentose, a phosphate, and a(n) ___.

     a. lipid                      b. acid

     c. nitrogen-containing base      d. amino acid


____6.  During the formation of a peptide linkage, which of the following occurs?

     a. a molecule of water is formed

     b. a disulfide bride is formed

     c. a hydrophobic bond is formed

     d. an ionic bond is formed


____7.  What is the nucleotide sequence of the complementary strand of this DNA molecule: AATGCGA?

     a. TTACGCT                         b. AATGCGA

     c. GGCATAG                         d. CCGTTAT


____8.  When a protein becomes nonfunctional as a result of a change in its environment, it is __________.

     a. permanent                  b. reversible

     c. denatured                  d. environmentalized


____9.  DNA carries genetic information in its _______.

     a. helical form                 b. sequence of bases

     c. tertiary sequence             d. sequence of amino acids

Biology 101 Chapter 4 The Organization of Cells



1.  List the two statements that define cell theory.

---all organisms are composed of cells

---all cells come from preexisting cells

   --the cell is the structural and functional unit of life

   --all living things are composed of one or more cells

   --cells can only come from preexisting cells

2.  Explain how surface area-to-volume ratio limits cell size.

---volume of cell determines amount of chemical activity it

   carries out per unit of time

---surface area determines amount of substances cell can

   take in for its environment and amount of wastes it can

   release to its environment

---surface area increases by the square while volume

   increases by the cube

---the KEY FACTOR limiting cell size is its surface area to

   volume ratio

---cells are small in volume in order to maintain a large

   surface area to volume ratio

3.  Distinguish between magnification and resolution.

---magnification describes how many times larger an object


---resolution describes the ability of a microscope to

   distinguish (resolve) two objects as being distinct or

   separate from each other

---as magnification increases, resolution tends to decrease

4.  Name and describe the two basic types of microscopes used by biologists.  Provide the advantages and limitations of each microscope type.

---compound light microscope and electron microscope

---compound light microscope

   --uses glass lenses and visible light

   --magnification up to 2000X and resolution of about

     0.2 um (1000X better than human eye)

   --allows visualization of cell sizes and shapes and some

     internal cell structures

   --latter difficult to see under ordinary light so cells

     often killed and stained with dyes = structures appear

---electron microscope

   --uses magnets to focus electron beams at fluorescent

     screen or photographic film to create visible image

   --mags up to 100,000X and resolution of 0.5 nm

     -250,000X finer than human eye


   --specific dyes and reagents that bind to specific types

     of molecules

5.  All cells possess a plasma membrane.  Describe the structure and function of the plasma membrane.

---plasma membranes separates (but does not insulate) cell

   from its environment

   --creates a segregated compartment

---composed of phospholipid bilayer embedded with proteins

---acts as selectively (semi) permeable barrier

---important in communicating with adjacent cells and

   receiving extracellular signals

---allows cell to maintain fairly constant internal

   environment (homeostasis)

6.  Distinguish between prokaryotic and eukaryotic cells on the following bases: Presence of a nucleus, presence of membrane bound organelles, presence of cytoskeleton.

---pro means “primitive” or “before” and karyote refers to

   “kernel” or nucleus

---prokaryotic cells do NOT have a nucleus, membrane

   bound organelles, or cytoskeleton

---organelle defined as a compartmentalized “special

   structure with specific functions” or “specific

   structure with special functions”

   --take your pick

   --concept is that an organelle can (will) do something

     nothing else in can (will) do

---“eu” in biology means “true”

---eukaryotic cells do have a nucleus, membrane bound

   organelles, and a cytoskeleton

7. List and describe the shared features of all prokaryotic cells.

---Domain Bacteria and Domain Archaea/Kingdom Monera

---plasma membrane encloses cell regulating traffic of

   materials in and out and separating it from environment

---region called the nucleoid contains DNA of cell

---rest of material enclosed in plasma membrane called

   the cytoplasm

   --cytoplasm composed of 2 parts: liquid cytosol and

     insoluble suspended particles including ribosomes

---cytosol composed of mostly water that contains dissolved

   ions, small molecules, and soluble macromolecules such

   as proteins

---ribosomes are granules/site of protein synthesis

   --70S ribosomes (50S large subunit; 30S small subunit)



8.  Describe the specialized features evident in some prokaryotic cells.

---SPECIALIZED FEATURES (not presence in all prokaryotes)

---most have cell wall located outside PM that is composed

   of peptidoglycan (polymer of amino sugars)

---some have outer membrane (polysaccharide rich

   phospholipid membrane) enclosing cell wall

---some have capsule which is layer of “slime” composed

   mostly of polysaccharides

   --capsule not essential to survival, but important in


---some prokaryotes (cyanobacteria & others) are


   --conversion of light energy into chemical energy

---some possess mesosomes which function in cell division

   or energy-releasing reactions

---some prokaryotes motile by means of flagella

   --flagellum composed of protein flagellin

---some will have pili which are much shorter and more

   numerous than flagella

   --threadlike structures used during “mating” and to

     adhere to animal cells for protection and/or food

9.  Explain the significance of compartmentalization in eukaryotic cells.

---eukaryotic cells have “cells within cells”

---interior compartments surrounded by membranes that

   regulate what enters and leaves that compartment

---membrane ensures conditions inside that compartment

   are different from those in surrounding cytoplasm

---some compartments are little factories that make

   specific products

---others are like power plants take in energy in one form

   and convert it to more useful form

---these membranous compartments (and other structures such

   as ribosomes that lack membranes but have distinctive

   shapes and functions) are called organelles

---each organelle has specific roles in cell

   --roles defined by chemical reactions

---nucleus, mitochondrion, endoplasmic reticulum, Golgi

   apparatus, lysosome, vacuole, and chloroplast

---all these organelles have unique chemical compositions

   and functions

---membrane surrounding does two things

   --keeps organelle’s molecules away from other molecules

     in cell

   --acts as traffic regulator


10. Describe the structure and function of the nucleus.

---most DNA in eukaryotic cell is stored in nucleus

---single nucleus usually largest organelle in cell

---site of DNA duplication (replication), site of DNA

   control of cellular activities, and region within

   nucleus called nucleolus begins assembly of ribosomes

   from specific proteins and RNA

---nucleus surrounded by bilayer membrane called the

   nuclear envelope

   --envelope perforated by nuclear pores

   --each pore surrounded by pore complex (8 large protein

        granules arranged in octagon where inner and outer

     membranes merge

---at certain places, envelope folds outward into cytoplasm

   and is continuous with the endoplasmic reticulum

---inside nucleus, DNA combines with proteins to form


   --chromatin can condense into chromosomes

---surrounding chromatin is the nucleoplasm

---within nucleoplasm is network of structural proteins

   called nuclear matrix which organizes the chromatin

---at periphery of nucleus, chromatin attaches to protein

   meshwork called nuclear lamina

   --helps maintain shape of nucleus

---during most of life cycle, nuclear membrane is stable


   --when cell divides, it fragments and reforms later

11. Describe the function of ribosomes.

---ribosomes are actual site of protein synthesis

---found in prokaryotes as granules in the cytoplasm

---found in eukaryotes in three places

   --floating free in cytoplasm, attached to surface of

     endoplasmic reticulum (rough ER) and within the

     mitochondrion (and chloroplast)

---consist of ribosomal RNA (rRNA) and proteins

12. List the components of the endomembrane system, describe their structures and functions, and summarize the relationship among them.

---endomembrane system includes 2 main components

   --endoplasmic reticulum and Golgi apparatus

---network of interconnected membranes branching throughout

   cytoplasm forming tubes and flattened sacs called

   endoplasmic reticulum (ER)

---interior compartment of ER called lumen is separate and

   distinct from surrounding cytoplasm

---at certain sites, ER is continuous with plasma membrane

---parts of ER sprinkled with ribosomes attached to outer

   faces of flattened sacs

   --ER with ribosomes attached is called rough ER (RER)

---most of proteins destined for export from cell are

   synthesized at rough ER

   --proteins enter lumen as synthesized and undergo

     modification and maturation (precursor)

   --some gain carbohydrate groups (glycoproteins) for

     addressing them to right parts of the cell

---cells that synthesize lots of proteins for export are

   usually packed with rough ER

   --glandular cells that secrete digestive enzymes and

     plasma cells that secrete antibodies

---some parts of ER, called smooth ER (SER) more tubular

   --SER lacks ribosomes

   --inside lumen of SER, some proteins made by RER are


   --responsible for modifying small molecules taken in by

     cell (like drugs and pesticides)

     -SER is detox center for the cell

   --is site for hydrolysis of glycogen and for synthesis

     of lipids

---Golgi apparatus consists of flattened membranous sacs

   called cisternae and small membrane-enclosed vesicles

   --cisternae appear like a stack of saucers

---is the UPS of the cell

---receives and modifies proteins from the ER

---concentrates, packages, and sorts proteins before


---where some polysaccharides for plant cell wall are made

---Golgi apparatus has 3 functionally distinct parts

---bottom cisternae (cis region) lie near nucleus or RER

---cisternae in middle make up medial region

---top cisternae (trans region) lie closest to surface of


---3 parts contain different enzymes and perform different


---part of ER buds off forming vesicle that contains

   precursor “product” and vesicle travels to Golgi appa.

   --fuses with membrane of GA and product enters GA

---vesicles are transport vehicles into and out of GA and

   to ultimate destinations of the proteins

13. Describe the functions of a lysosome.

---lysosomes originate in part from the GA

---contain very potent digestive enzymes and are site

   of hydrolysis of macromolecules to their monomers

---surrounded by single membrane

---are sites for breakdown of food and foreign objects

   taken up by cell

---chalk talk and phagocytosis

---phagosome-->fuses with primary lysosome-->secondary


---lysosomes where cell digests its material in process

   called autophagy

   --ongoing process for recycling of damaged and worn-out


---plant cells do NOT contain lysosomes; central vacuole

   contains digestive enzymes

14. Describe the structure and function of a mitochondrion.

---primary function is to convert potential chemical energy

   of food molecules into form cell can use (ATP)

---commonly called the “powerhouse of the cell”

---in mitochondrion, production of ATP using fuel molecules

   and O2 called cellular respiration

---have two membranes: outer and highly folded inner

   membrane called cristae

---cristae encloses the mitochondrial matrix

   --matrix contains many proteins, some ribsomes, and DNA

15. Explain why compartmentalization is important to mitochondrial function.

---outer membrane is smooth and protective and offers

   little resistance to substances moving in and out

---inner membrane contains proteins needed for cellular

   respiration (electron transport chain)

---inner membrane exerts much more control over what enters

   and leaves mitochondrion than does outer membrane

---number of mitochondria in cell varies with energy

   requirements of cell

---double membrane structure important for ETC, [ ]

   gradient, and electrical potential across membrane

16. Differentiate between chloroplasts, chromoplasts, and leucoplasts.

---all are plastids and are found only in plants and

   certain protists

---chloroplasts most familiar of the plastids

   --contains green pigment chlorophyll and is site of


---chromoplasts are red, orange, or yellow depending on

   type of carotenoid pigments present

   --have no known chemical function in cell

   --colors they give to petals and fruits help attract

     pollinators and aid in seed dispersal

---leucoplasts are storage depots for starch and fats



17.  Describe the structure and function of a chloroplast.

---outer membrane, inner membrane, and membranous sacs

   called thylakoids

---thylakoids arranged in stack called granum (short stack)

   --more than one granum = grana

---grana suspended in thick fluid called stroma

   --stroma contains ribosomes and DNA

---chloroplasts are site of photosynthesis

---light reactions occur in thylakoid membrane

---dark reactions occur in the stroma

---animal cells do not produce chloroplast but some may

   contain functional chloroplasts

   --derived from partial digestion of green plants

   --contained within unicellular algae that live within

     animal’s tissues (green color of some corals and

     sea anemones) result from chloroplasts in algae that

     live within those animals

18. Describe the function of a peroxisome.

---found at one time or another in some of cells of every


---small organelles with single membrane & contain enzymes

   to detoxify the toxic peroxides (hydrogen peroxide)

   --peroxides formed as side products of chemical


---broken down within peroxisome within mixing with other

   parts of the cell

---glyoxysome is structurally similar plant organelle

   --sites where stored lipids are converted into carbos

     for transport to growing plant cells

19. List and explain the functions of vacuoles, including food vacuole, contractile vacuole, and central vacuole.

---many eukaryotic cells (plant/protists) contain membrane

   enclosed organelles that look empty under the EM

---these organelles are called vacuoles

---are filled with aqueous solutions that contain many

   dissolved substances

---plants can secrete some toxic by-products but most are

   stored in vacuoles

   --poisonous/distasteful and help deter some animals from

      eating the plant

   --stored wastes may contribute to plant survival

---plant cells have large central vacuole

---dissolved substances in vacuole help provide turgor or

   stiffness of cell which provides support for nonwoody


---osmosis and turgor pressure

---play role in “sex-life” of plant


   --some pigments (blue/pink) in petals and fruits stored

     in vacuoles

   --these pigments are called anthocyanins

---food vacuoles found in some single-celled protists and

   simple animals like sponges

   --cells engulf food by phagocytosis generating a food


   --fusion of food vacuole with lysosome = digestion

---many freshwater protists have contractile vacuole

   --function is to rid cell of excess water

   --chalk talk time and ye humble Paramecium

20. Provide three important roles for the cytoskeleton.

---eukaryotic cytoplasm has set of long, thin fibers called

   the cytoskeleton

---fills three important roles

   --maintains cell shape and support

   --provides for various types of cell movement

   --some of its fibers act as tracks or support for motor

      proteins which help cell move or move things within


21. Differentiate among microtubules, microfilaments, and intermediate filaments.

---microfilaments can exist as single filaments, bundled,

   or in networks

---assembled from protein actin

   --extensively folded with distinct “head” and “tail”

   --interact with other actin molecules to assemble into

     long chain

   --two of these chains form double helix of microfilament

---have two major roles

   --help entire cell or parts of cell to contract

   --stabilize cell shape

---in muscle cells actin fibers associated with myosin

   --accounts for contraction of muscle cells

---involved in cytoplasmic streaming & cleavage furrow

---involved with pseudopodia

---support tiny microvilli that line intestine

---help RBC maintain its familiar doughnut shape

---intermediate filaments found only in multicellular


   --five distinct types all composed of keratin

---organized into tough, ropelike assemblages

---have two major functions

   --stabilize cell structure

   --resist tension


---often radiate from nuclear envelope and help maintain

   positions of nucleus and other organelles within cell

---help connect spot welds called desmosomes between

   adjacent cells

---microtubules are long, branched cylinders composed of


--have two major roles

   --form rigid internal skeleton for some cell

   --act as framework on which motor proteins can move

     structures in the cell

---can change length rapidly by adding/subtracting tublin

   dimers at the + end

---many microtubules radiate from microtubule organizing


---in plant cells, help control arrangement of cellulose

   fibers of cell wall

---can serve as tracks for motor proteins

---are essential in distributing chromosomes to daughter

   cells during cell division

---are intimately associated with cilia and flagella

22. Differentiate between cilia and flagella and describe their internal structure.

---cilia and eukaryotic flagella are assembled from

   microtubules and have identical internal structures

---push or pull cell through environment or move

   surrounding liquid over surface of cell

---flagella are longer than cilia and usually found singly

   or in pairs

   --beat in wavelike motion

---cilia are shorter than flagella and much more numerous

   --beat stiffly in one direction and recover flexibly in

        other direction so recovery stroke does NOT undo work

     of power stroke

---contains 9 + 2 arrangement

---in cytoplasm at base of every eukaryotic flagellum or

   cilium is organelle called a basal body

   --have nine fused microtubule triplets but no inner


---flagellum, hook, basal body

---centrioles are almost identical to basal bodies

   --found in all eukaryotic cells except flowering plants,

     pine trees & relatives, and some protists

   --seem to be important in formation of spindle fibers

23. Describe the structure of the plant cell wall.

---extracellular structures are outside plasma membrane

   --produced by cell and secreted

---cell wall of plants is semirigid structure outside PM

---consists of cellulose embedded in complex


---cell wall has two major roles

   --provides support for cell and limits its volume by

     remaining rigid

   --acts as barrier to infections by fungi/other organisms

     that cause plant diseases

---cytoplasm of adjacent plant cells connected by plasma-

   membrane lined channels called plasmodesmata

   --permits diffusion of water, ions, small molecules,

     RNA, and proteins between connected cells


Additional Objectives for this Chapter


24. Discuss the extracellular matrix of animal cells.

---composed of fibrous proteins (collagen) and


---serve many functions

   --hold cells together in tissues

   --contributes to physical properties of cartilage,

     skin, and other tissues

   --helps filter materials passing between tissues

   --helps orient cell movement during embryonic

     development and during tissue repair

   --plays role in chemical signaling from one cell to



Biology 101 Chapter 4

Student Self Assessment Short Answer


1.  A measure of the smallest distance that distinguishes two individual objects is the ______________________.


2.  In biology, the basic unit of life is called a(n) ___________________.


3.  ________________ is the process whereby light energy is converted into chemical bonds.


4.  The ______________  ___________________ is an organelle that serves as a sort of “postal depot” where some of the proteins synthesized on ribosomes and rough ER are processed.


5.  All organisms are composed of cells; all cells come from preexisting cells.  These statements are called the _______________  _______________________.


6.  The DNA in a prokaryotic cell can be found in the ______________________ region.


7.  Steroids, fatty acids, phospholipids, and carbohydrates are synthesized in the ______________  ___________________.


8.  Toxic peroxides that are unavoidably formed as side products of important cellular reactions are found and neutralized in ______________________.


9.  The __________________ is the cytoskeletal component with the smallest diameter.


10. When one cuts an orange in half, one _______________ the surface area-to-volume ratio.



Biology 101 Chapter 4

Student Self Assessment Multiple Choice


____1.  The utilization of “food” in the mitochondria, with the associated formation of ATP, is termed ______________________.

     a. cellular respiration         b. metabolic rate

     c. diffusion                  d. catabolism


____2.  Components of chloroplasts include ______.

     a. grana                      b. thylakoids

     c. cristae                         d. a and b


____3.  All members of the kingdom Eubacteria _____.

     a. have nuclei                     b. have chloroplasts

     c. are multicellular             d. are prokaryotes


____4.  Some bacteria are able to propel themselves through liquid by means of a structure called the ___________.

     a. flagellum                  b. pili

     c. cytoplasm                  d. cell wall


____5.  Which of the following is a general function of all cellular membranes?

     a. They regulate which materials can cross the membrane.

     b. They support the cell and determine its shape.

     c. The produce energy for the cell.

     d. The produce proteins for the cell.


____6.  The two major types of cells are _______.

     a. human and nonhuman             b. blood and muscle

     c. prokaryotic and eukaryotic     d. plant and animal


____7.  The one type of cell that is always lacking a cell wall is the ______ cell.

     a. bacterial                  b. plant

     c. animal                          d. fungal


____8.  Of the following structures, the one that contains both a matrix and a cristae is the _____.

     a. plastid                         b. lysosome

     c. Golgi apparatus            d. mitochondrion


____9.  Light energy for conversion to chemical energy is trapped in the ________________.

     a. mitochondrion                  b. chromoplast

     c. thylakoid                  d. endoplasmic reticulum


____10. Ribosomes are made up of _____.

     a. DNA and RNA                  b. DNA and proteins

     c. RNA and proteins             d. proteins

Biology 101 Chapter 5 Cellular Membranes



1.  Describe the functions of the plasma membrane.

---chemical makeup, physical organization, and functioning

   of biological membrane depend on three classes of

   biochemical compounds

   --lipids, proteins, and carbohydrates

---plasma membrane composed of hydrophobic lipid bilayer

---function is to regulate what enters and leaves the


---are dynamic structures whose components move, change,

   and perform vital functions

---allow cells to interact with other cells and molecules

   in their environment

---regulate ionic and molecular traffic into/out of cell

2.  List the components that comprise the plasma membrane.

---lipids establish the physical integrity of membrane

---create effective barrier to rapid passage of hydrophilic

   materials such as water and ions

---phospholipid bilayer serves as “lake” in which variety

   of proteins “float”

   --general design known as fluid mosaic model

---membrane proteins function in moving materials through

   membrane and receiving chemical signals from cell’s

   external environment

---carbohydrates in membrane are crucial in recognizing

   specific molecules

   --carbos attach to either lipid or protein molecules on

     outside of plasma membrane where they protrude into


3.  Describe the fluid properties of the cell membrane and explain how fluidity is influenced by membrane composition.

---phospholipid bilayer has hydrophilic heads and

   hydrophobic tails

---stabilizes the entire membrane structure

---fatty acid tails make the hydrophobic interior of

   membrane somewhat fluid (light weight machine oil)

---fluidity permits some molecules to move laterally within

   plane of membrane

---often cholesterol present in membrane (25% common)

---cholesterol may increase or decrease fluidity

---shorter fatty acid tails and unsaturated fatty acids

   make for more fluidity

---adequate membrane fluidity is essential for many

   membrane functions

---fluidity decreases at reduced temperatures

4.  Describe how proteins are spatially arranged in the cell membrane and how they contribute to membrane function.

---all biological membranes contain proteins but numbers

   vary greatly

---many proteins are embedded in, and/or extend across the

   lipid bilayer

---like phospholipids, proteins have polar and nonpolar


---proteins and lipids in membrane are independent of each


---integral proteins penetrate the bilayer

---peripheral proteins are embedded in either top or bottom

   layer of phospholipid bilayer

---some proteins free to move throughout layer; others seem

   to be anchored by components of cytoskeleton

---example is protein associated with motor junction of

   muscle cells

---two surfaces of bilayer have different membrane


---important in moving, reception of chemical signals, and

   in recognition

5.  Describe the factors that affect selective permeability of membranes.

---membrane is permeable to solutes/solvents that can cross

   it more or less easily

---said to be impermeable to substances that cannot cross

---membrane permeability influenced by fluidity of

   membrane, numbers and kinds of proteins embedded in it,

   temperature, and concentration gradient of substances

   across membrane

6.  List and describe the functions of the following cell junctions: Tight junctions, desmosomes, and gap junctions.

---tight junctions are specialized structures at PM that

   link adjacent epithelial cells

---are found in region surrounding lumen of cavity of

   organs such as intestine

---have 2 functions

   --prevent substances from moving through intercellular

     space; requires any substance entering body from lumen

     must pass through epithelial cells

   --restrict migration of phospholipids and membrane

     proteins from one region of PM to another

   --region facing lumen can be different from region

     facing sides and bottom of cell

---help ensure the directional movement of materials into

   the body


---desmosomes are specialized structures associated with

   PM at certain sites in epithelial tissue

---hold adjacent cells firmly together (spot welds)

---cytoplasmic fibers of desmosomes (intermediate filaments

   of cytoskeleton) made of protein called keratin

---provide great mechanical stability to epithelial tissues

---gap junctions facilitate communication between cells

---each gap junction composed of protein channels called

   connexons that span the PMs of two adjacent cells and

   the intercellular space between them

7.  List the types of passive and active transport.

---passive transport include different kinds of diffusion

   --simple and facilitated diffusion

---active transport

   --primary and secondary active transport

8.  Define diffusion; explain what causes it and why it is a spontaneous process.

---diffusion is the process of random movement toward a

   state of equilibrium

---result of the kinetic energy of atoms/molecules

---motion of each particle is random, but in diffusion

   the net movement of particles is directional until

   equilibrium is reached

---diffusion is NET movement from regions of greater [ ]

   to regions of less [ ]

---diffusion of one substance is independent of others

---how fast substance moves depends on four factors

   --diameter of the molecules or ions

   --temperature of the solution

   --electrical charge (if any) of diffusing material

   --concentration gradient in the system

     -CG is change in [ ] with distance in given direction

     -greater the CG, more rapidly substance diffuses

---is spontaneous process because of kinetic energy

---simple diffusion allows small molecules to pass through

   lipid bilayer of PM

---more lipid soluble the molecule, the faster it diffuses

   --only water and smallest molecules are exception

---charged and/or polar molecules (amino acids, sugars,

   and ions) do no pass readily through membrane

9.  Define osmosis and predict the direction of water movement based upon differences in solute concentration.

---solute, solvent, and solution time

---osmosis defined as the movement of water molecules

   across a selectively permeable membrane

   --not quite true, but will do for our course


---is simple diffusion and is based on the [ ]s of


---depends on number of solute particle present and not the

   kind of particles

---RBCs and plasma; “fresh” celery from the grocery store

---water will always move (if it can) down its [ ] gradient

   --toward solution with higher solute [ ]

---chalk talk time with hyper, hypo, and isotonic

---water always moves from hypotonic to hypertonic solution

---**remember reference is to NET movement of water

10. Describe how living cells with and without water regulate water balance.

---[ ] of solutes in environment determines direction of

   osmosis in animal cells (NO CELL WALLS)

   --crenation, hemolysis, or all is well

---cells of plants, archaea, bacteria, fungi, and some

   protists have cells walls that limit volume of cells and

   keep them from bursting in placed in hypotonic solution

---cells with sturdy cell walls take up limited amount of

   water & build up internal pressure against cell wall

   that prevents further water from entering

   --called turgor pressue

---cell with cell wall placed in hypertonic solution loses


   --PM pulls away from cell wall = plasmolysis

   --sometimes reversible otherwise...Auf wiedersehen

11. Describe facilitated diffusion and determine why it is not active transport.

---polar substances do not diffuse across membranes

---cross hydrophobic lipid barrier through protein-lined

   channels in process called facilitated diffusion

---best studied are ion channels

   --are gated, can be open or closed to ion passage

   --open when something happens to change shape of protein

---movement of water into and out of cell is aided by

   aquaporins (membrane proteins that allow water to pass)

---another kind of facilitated diffusion requires actual

   binding of transported substance to membrane protein

   --carrier proteins allow diffusion into and out of cell

---glucose transport classic example (glucose transporter)

---facilitated diffusion system subject to saturation

---facilitated diffusion NOT active transport because it

   requires NO expenditure of energy by cell

12. Explain how active transport differs from diffusion.

---substances diffuse down their [ ] gradient

---active transport moves substances against their [ ]


---movement of a substance across biological membrane

   against a [ ] gradient is called active transport

   and requires the expenditure of energy and a

   transport membrane

---three types of proteins are involved in active transport

   --uniport moves single solute in one direction (Ca2+)

   --symport move 2 solutes in same direction (AA & Na+)

   --antiport move 2 solutes in opposite directions

     (Na+-K+ pump; two K+ in and three Na+ out)

---two types of active transport: primary and secondary

---primary requires direct participation of ATP

---only CATIONS are transported directly in primary AT

---other solutes are transported by secondary AT

   --does not use ATP directly

---transport of solute is coupled to ion [ ] gradient

   established by primary AT

   --sodium ions and glucose molecules

---both symports and antiports are used in secondary AT

13. List and describe the three processes used in endocytosis.

---endocytosis general term for group of processes that

   bring macromolecules, large particles, small molecules,

   and cells into eukaryotic cell

---three types of endocytosis: phagocytosis, pinocytosis,

   and receptor-mediated endocytosis

---plasma membrane invaginates around material from

   environment forming small pocket-->vesicle-->separates

   from PM and moves with contents into cell’s interior

---phagocytosis (cellular eating) used to engulf large

   particles or even entire cells

   --used by unicellular protists (lunch) and by WBCs

   --food vacuole/phagosome fuse with lysosome = digestion

---pinocytosis (cellular drinking) used to bring in

   small dissolved substances or fluids

   --relatively nonspecific in what it brings in

   --endothelium (single layer of cells that separates tiny

     capillary from surrounding tissue

---receptor-mediated endocytosis used to capture specific

   macromolecules from environment

---requires receptor proteins at particular sites on outer

   surface of PM

   --these sites are called coated pits

   --once bound, substance is coated and carried inside

   --is method by which cholesterol taken up by most

     mammalian cells

   --hypercholesterolemia anyone?


14. Define exocytosis.

---is process by which materials packaged in vesicles are

   secreted from cell when vesicle fuses with PM

---important as last step in processing materials engulfed

   by phagocytosis

---important in secretion of many different substances

   including digestive enzymes, neurotransmitters, and

   materials for construction of plant cell wall

15. Explain why the plasma membrane cannot be called a static process.

---plasma membrane important in information processing,

   energy transformations, and organizing chemical


---membranes continually form, move, and fuse in cells

---PM altered by endocytosis and exocytosis




Biology 101 Chapter 5

Student Self Assessment Short Answer


1.  The ______________ molecules of membranes act as barriers to passage of many materials and serve to maintain the membrane’s physical integrity.


2.  In a complex solution, the _______________ of each substance is independent of that of the other substances.


3.  ______________-____________  _____________ is the movement of specified macromolecules into a cell; it involves coated pits, clathrin, and coated vesicles.


4.  Some materials move through biological molecules more readily that others.  This characteristic of biological membranes is called selective ___________________________.


5.  One places a cell into a solution and the cell shrinks.  This solution is ___________________ relative to the cell.


6.  Diffusion occurs _______________ a concentration gradient.


7.  Three things that influence diffusion rate are the __________  ____  _______________, ___________________, and the ___________________  _______________________.


8.  The force that increases inside a plant when it is placed in water, which finally prevents further net movement of water molecules into the cell, is called _______________________ pressure.


9.  Biological membranes are organized in the manner described by the _____________  __________________ model.


10. The process of one cell engulfing another is called __________________________________.



Biology 101 Chapter 5

Student Self Assessment Multiple Choice


____1.  Specialized cell junctions include _______.

     a. gap junctions                  b. tight junctions

     c. desmosomes                 d. all of the above


____2.  Substances move through biological membranes against concentration gradients via ____________.

     a. simple osmosis              b. active transport

     c. reverse osmosis              d. facilitated diffusion


____3.  The interior of the phospholipid bilayer is _____.

     a. hydrophilic                    b. hydrophobic

     c. aqueous                         d. charged


____4.  A protein that forms an ion channel through a membrane is most likely to be ________.

     a. a peripheral protein         b. an integral protein

     c. a phospholipid              d. an enzyme


____5.  When a red blood cell is placed in an isotonic solution, which of the following things will occur?

     a. the cell will shrivel         b. the cell will swell and burst

     c. the cell will shrivel and then return to normal

     d. nothing


____6.  Osmosis is a specific form of _______.

     a. diffusion                  b. facilitated transport

     c. active transport            d. secondary active transport


____7.  Transport proteins that simultaneously move two molecules across a membrane in the same direction are called _______.

     a. uniports                   b. symports

     c. antiports                  d. diffusive ports


____8.  Connexons occur in ______.

     a. the cytoskeleton              b. tight junctions

     c. desmosomes                 d. gap junctions


____9.  Secondary active transport involves all the following EXCEPT __.

     a. the direct use of ATP

     b. coupling to another transport system

     c. use of regained energy from an existing gradient

     d. the ability to concentrate the transported molecule


___10. Biological membranes are composed of _____.

     a. nucleotides and nucleosides

     b. enzymes, electron carriers, and electron donors

     c. fatty acids

     d. lipids, proteins, and carbohydrates

Biology 101 Chapter 6

Energy, Enzymes, and Metabolism


1.  Explain the role of catabolic and anabolic pathways in the energy exchanges of cellular metabolism.

---metabolism is the sum total of all the chemical

   conversions in a cell

---metabolism divided into two units; anabolism and


---anabolism is concerned with building up complexity

   in the cell and using energy to do so

---catabolism is concerned with breaking down complex

   substances into simpler ones and releasing energy in

   the process

---the reactions are often linked

2.  Explain, in your own words, the First and Second Law of Thermodynamics.

---energy defined as the ability to do work

   --work defined as movement of mass through space

---kinetic energy versus potential energy

---in biochemistry, energy represents capacity for change

---First Law states that energy cannot be created nor


   --it can be converted from one form to another

   --chemical to light; mechanical to electrical, potential

     to kinetic and vice versa

---law applies to the universe or any closed system

   --closed system is one that is NOT exchanging energy

     with its surroundings

---open system merely one part of a larger closed system

---First Law states that in any interconversion, the total

   energy before and after the conversion is the same

---Second Law that although energy cannot be created nor

   destroyed, when energy is converted from one form to

   another, some of the energy becomes unavailable to do


---**no energy conversion is every 100%

   --some lost to entropy (disorder) and some lost as heat

---in biological systems, total energy called enthalpy (H)

---usable energy that can do work called free energy (G)

---unusable energy represented by entropy (S) which is

   multiplied by the absolute temperature

   --H = G + TS

   --can be rewritten to G = H – TS

---energy changes measured as calories (cal) or joules (j)

---change in value represented by Greek letter Δ (delta)

   and can be negative or positive

   --ΔG = ΔH – TΔS

---equation tells us if free energy is released or consumed

   by chemical reaction

---if ΔG is negative, free energy is released

   --if positive, free energy is consumed
---endergonic versus exergonic reactions

3.  Describe the function of ATP in the cell.

---ATP is the energy coin of the realm

---adenosine triphosphate

---it can be hydrolyzed and it can donate a phosphate group

   to many different molecules

---ADP--->ATP cycle

   --couples exergonic and endergonic reactions

---40 kg per day for average person at rest

4.  List the three components of ATP and identify the major class of macromolecules to which it belongs.

---belongs to the nucleic acids

---can readily be converted into building block for either

   DNA or RNA

---contains the nitrogenous base adenine, five-carbon sugar

   ribose, and three phosphate groups

5.  Explain how ATP performs cellular work.

---phosphate groups are negatively charged

   --takes lot of free energy to overcome tendencies of

     phosphates to repel each other

---energy invested to make ADP from AMP and to make ATP

   from ADP

---when phosphate removed, energy required to “put it

   there” is released and used to do cellular work

---active cell requires millions of ATP molecules per

   second to drive its machinery

6.  Describe how an enzyme affects the rate and the activation energy of a chemical reaction.

---catalyst is any substance that speeds up chemical

   reaction without itself being used up

---most biological catalyst are proteins called enzymes

   --certain RNA molecules (ribozymes) also catalytic

---reactions would proceed eventually given infinity

   --not fast enough or often enough to sustain life


---coenzymes and cofactors

---for reaction to proceed, energy barrier must be overcome

---“exergonic reactions proceed only after they are pushed

   over energy barrier by small amount of added energy”

   --needed energy is called activation energy (EA)

   --EA changes reactants into unstable molecular forms

     called transition-state species

---could lower activation energy by increasing temperature

   --sucrose and Bunsen for a light?

---enzymes work by lowering activation energy so reaction

   can proceed at temperatures favorable to life

---some can catalyze 400 million reactions per second

   --liver enzyme catalase

7.  Explain the specificity of binding between an enzyme and its substrate (induced fit).

---in enzyme-catalyzed reaction, the reactants are called


---substrates bind to a particular site on the enzyme

   surface called the active site

---specificity of an enzyme results from the exact three

   dimensional shape and structure of its active site

---reason enzyme recognizes it substrate is because “it


---most enzyme names end in “ase”

---binding of substrate to its enzyme produces the

   “enzyme-substrate” complex, reaction is catalyzed,

   product(s) are released because they no longer “fit”

---enzyme-substrate complex held together by hydrogen

   bonds, ionic attraction, or covalent bonding

---enzymes lower the activation energy required for the

   reaction by one or more processes

   --enzymes orient substrates

   --enzymes add charges to substrates

   --enzymes induce strain in the substrate

---we need to briefly discuss competitive and

   noncompetitive inhibition of enzymes

---two models for enzyme specificity

   --lock and key model and induced fit model

     -induced fit is currently most accepted model

---enzymes are flexible and their active sites can change

   (expand) to fit substrates

---when substrate binds, enzyme changes shape, exposing the

   parts of itself that react with the substrate

---change of enzyme shape caused by substrate binding is

   called induced fit

8. Explain how substrate concentration, temperature, and pH affect the rate of an enzyme-controlled reaction.

---if no enzyme present, the rate of reaction would be

   directly proportional to the concentration of substrate

   -->higher the [ ] the more collisions = more reactions

---addition of enzyme speeds up the reaction and changes

   shape of plot of the reaction

   --rate increases as substrate increases but then levels


---enzyme has become saturated (working as fast as it can)

---turnover number describes how many molecules of

   substrate are converted to product in one second

---when enzyme is saturated, adding additional substrate

   will NOT increase reaction rate any further

---most enzymes have optimal ph range

   --activity decreases if solution made more acidic or

     more basic than its ideal pH

---temperature affects enzyme activity

   --warming will speed up enzyme-catalyzed reactions

   --only to a certain point

---temperature becomes too warm and enzyme begins to

   denature (nonfunctional)

---many organisms make isozymes (enzymes that catalyze

   same reaction but have different optimal temperatures




Biology 101 Chapter 6

Student Self Assessment Short Answer


1.  Enzymes are biological ___________________________.


2.  When an enzyme is heated until its three-dimensional structure is destroyed, the enzyme is said to be ______________________.


3.  ______________ is the term used for all the chemical activity of a living organism.


4.  The building up of molecules in a living system is ____________________, while the breaking down is ___________________.


5.  The first law of thermodynamics is that ___________________________________________________________(short phrase).


6.  Variations of enzymes that allow organisms to adapt to changing environments are termed ________________________.


7.  Most of the Earth’s energy comes from the _______________________________.


8.  Cells mostly use _____________________ as an immediate source of energy to drive reactions.


9.  A(n) _______________ reaction, where one reaction is used to drive another, is the major means of carrying out energy-requiring reactions within cells.


10. The second law of thermodynamics states that the __________________, or disorder, of the universe is constantly increasing.


11. The enzyme phosphoglucoisomerase catalyzes the conversion of glucose 6-phosphate to fructose 6-phosphate.  The region on phosphoglucoisomerase where glucose

6-phosphate binds is called the _____________  ___________.



Biology 101 Chapter 6

Student Self Assessment Multiple Choice


____1.  End products of biosynthetic pathways often act to block the initial step in that pathway.  This phenomenon is called __________.

     a. allosteric inhibition      b. denaturation

     c. binary inhibition           d. feedback inhibition


____2.  Competitive and noncompetitive enzyme inhibitors differ with respect _______________.

     a. the precise location on the enzyme to which they bind

     b. their pH

     c. their binding affinities

     d. their energies of activation


____3.  The first law of thermodynamics states that the total energy in the universe is ________.

     a. decreasing                 b. increasing

     c. constant                   d. being converted to matter


____4.  The molecules that are acted upon by an enzyme are called ___.

     a. products                   b. substrates

     c. carriers                   d. effectors


____5.  The sum of all the chemical reactions in a living structure is called its ____________.

     a. energetics                 b. activity

     c. digestive power           d. metabolism


____6.  An active site is ____.

     a. the part of the substrate that binds with an enzyme

     b. the part of the enzyme that binds with a substrate

     c. where energy is added to an enzyme catalyst

     d. where enzymes are found in cells


____7.  The diversity of chemical reactions occurring in a cell depends mostly on certain molecules present in the cell termed ___.

     a. isozymes                   b. coenzymes

     c. ribosomes                  d. enzymes


____8. When organisms move from one environment to another, they sometimes synthesize variations of existing enzymes termed ____.

     a. coenzymes                  b. abzymes

     c. isozymes                   d. effectors


____9.  The fact that an enzyme’s active site can sometimes bind inhibitors that are larger than the substrate is called _____.

     a. induced fit                  b. enzyme flex

     c. lock and key paradox         d. enzyme retrofit




Biology 101 Chapter 7

Cellular Pathways that Harvest Chemical Energy



1.  List the principles that govern metabolic pathways of the cell.

---complex chemical transformations in cell do NOT occur

   in single reactions but in a number of small steps that

   are connected in a pathway

---each reaction is catalyzed by a specific enzyme
---metabolic pathways are similar in all organisms

---many metabolic pathways are compartmentalized with

   certain steps occurring inside an organelle

---metabolic pathways are regulated by the activities

   of a few enzymes

2.  Explain why glucose is studied as the fuel for cellular respiration.

---glucose is MOST COMMON fuel for living cells

---many other compounds serve as food

   --almost all are converted to glucose or to intermediate


---cells obtain energy from glucose by the chemical process


3.  Write and describe the balanced equation for cellular respiration.

---if glucose is burned in a flame, it forms carbon dioxide

   and water, and lots of energy

   --but ONLY if oxygen gas (O2) is present

---C6H12O6 + 6 O2 ---> 6 CO2 + 6 H2O + energy

   --energy is in form of heat and light

---same equation applies to metabolism of glucose in cells

   except that metabolism is a multi-step controlled series

   of reactions

   --captures about 40% of energy in form of ATP

---complete oxidation of glucose = -686 kcal/mol

   --highly exergonic and can drive endergonic formation

     of ATP from ADP and phosphate

---some kinds of cells, unable to obtain or use oxygen

   gas, metabolize glucose incompletely and obtain LESS

   ATP per glucose

4.  List and briefly describe the three metabolic pathways by which glucose may be oxidized.

---glycolysis (splitting of sugar) is series of reactions

   that begins metabolism of glucose in ALL cells

   --called “universal pathway”

   --produces three-carbon compound called pyruvate

       (pyruvic acid)

   --small amount of ATP and NADH are produced

   --NADH is an electron carrier (NAD+ to NADH)

---cellular respiration occurs when environment is

   aerobic (contains oxygen gas, O2)

   --converts pyruvate into carbon dioxide (CO2)

   --includes “preparatory Krebs,” Krebs, and ETC

   --great deal of energy stored in covalent bonds of

     pyruvate is released and trapped in ATP

---fermentation occurs when the environment is anaerobic

   (lacking oxygen gas)

   --instead of energy poor CO2, relatively energy rich

     molecules (lactic acid or ethanol) are produced

   --energy extracted from glucose is much less than under

     aerobic conditions

---true fermenters must exist on 2 ATP (net) per glucose

   --ever see a 160 lb yeast cell?

5.  Define oxidation and reduction in relation to electron loss or gain.

---a reaction in which one substance transfers one or more

   electrons to another substance is called an oxidation-

   reduction reaction (redox for short)

---the gain of one or more electrons by an atom, ion, or

   molecule is called reduction

---the loss of one or more electrons by an atom, ion, or

   molecule is called oxidation

---defined in terms of traffic in electrons, can also think

   in these terms when hydrogen atoms are gained/loss

---oxidation-reduction ALWAYS occur together

---reactant that becomes reduced is an oxidizing agent

   and reactant that becomes oxidized is a reducing agent

---you will need to think about this for it to make sense

---in redox reactions, energy is transferred

---some of key reactions in glycolysis and cellular

   respiration are highly exergonic redox reactions

6.  Explain how redox reactions are involved in energy transfers.

---some of energy in reducing agent (one that is oxidized)

   is transferred to oxidizing agent (one that is reduced)

---main pair of oxidizing and reducing agents in cells is

   based on NAD (nicotinamide adenine dinucelotide)

---NAD+ is oxidized form and NADH is reduced form

---FAD is another electron carrier of importance

---redox reactions important in glycolysis, preparatory

   Krebs, Krebs, and the electron transport chain

7.  Define coenzyme and list those involved in respiration.

---coenzyme is nonprotein molecule that plays role in

   catalysis by an enzyme

   --may be part of the enzyme molecule or free in solution

   --some coenzymes are oxidizing or reducing agents


8.  List the metabolic pathways involved in the oxidation of glucose when oxygen is used as the final electron acceptor.

---when O2 is available as final electron acceptor, four

   pathways operate

---glycolysis takes place first followed by the three

   pathways of cellular respiration

---pyruvate oxidation (preKrebs), citric acid cycle (Krebs)

   and respiratory chain (electron transport chain)

9.  List the metabolic pathways that may occur if oxygen is NOT used as the final electron acceptor.

---when O2 is unavailable, pyruvate oxidation, the citric

   acid cycle, and the respiratory chain do NOT function

   and fermentation is added to the pathway

10. Write a summary equation for glycolysis and describe where it occurs in the cell.

---glucose--->2 pyruvate + 2 ATP (net) + 2 NADH

---glycolysis known as universal pathway

---occurs in cytoplasm of cell and DOES NOT require

   presence of O2

---has energy investment stage of 2 ATP

---chalk talk time for glycolysis

11. Describe where pyruvate is oxidized to acetyl CoA, what molecules are produced and how it links glycolysis to the Krebs cycle.

---two 3-carbon molecules of pyruvate produced by

   by glycolysis are in cytoplasm of cell

---in eukaryotes, they must be moved into mitochondrion

---enormous enzyme complex for pyruvate oxidation is

   attached to inner mitochondrial membrane

---pyruvate is oxidized to the acetyl group, and CO2 is


---part of energy from oxidation in first step is saved by

   reduction of NAD+ to NADH + H+

---some of remaining energy is stored temporarily by

   combining the acetyl group with CoA

---oxidation of pyruvate to acetate is link between

   glycolysis and cellular respiration

   --pyruvate cannot enter Krebs cycle

---chalk talk time on preparatory Krebs (oxidation of




12. Describe the location, the molecule that enters, and molecules that exit the Krebs cycle.

---Krebs cycle occurs in mitochondrial matrix

---acetyl-CoA is starting point for Krebs cycle

---chalk talk time on Krebs cycle (citric acid cycle)

---principal inputs into cycle are acetate (acetyl-CoA),

   water, and oxidized electron carriers (NAD+ & FAD)

---principal outputs are carbon dioxide and reduced

   electron carriers

---also yields 2 ATP by substrate-level phosphorylation

13. Describe the three steps that explain the fate of NADH and FADH2 in the respiratory chain.

---respiratory chain (electron transport chain) located

   in inner mitochondrial membrane

---first, electrons pass through series of membrane-

   associated electron carriers called respiratory chain

---second, as electrons flow along the chain, redox

   reactions provide energy to actively pump protons across

   inner mitochondrial membrane, out of matrix, creating

   a larger [ ] gradient and increasing the membrane

   potential (charge across the membrane)

---third, the protons diffuse back into matrix through

   protein channel (ATP synthase) which couples this   

   diffusion to the synthesis of ATP

---**type of ATP synthesis resulting from electron

   transport through respiratory chain is called

   oxidative phosphorylation

14. Explain how chemiosmosis couples the active transport of hydrogen ions and the production of ATP.

---chalk talk on chemiosmosis

---each NADH traded (on average) for 3 ATP

---each FADH2 traded for 2 ATP

---critical thinking time, why is NADH worth 3 ATP and FADH2  

   only worth 2 ATP?

15. Explain how membrane structure is related to membrane function in chemiosmosis.

---mitochondrion has two membranes, outer and inner

   --this creates an intramembranous space essential for

     establishment of both [ ] gradient for H+s and for

     increasing membrane potential across inner membrane

   --called proton-motive force

---inner membrane is highly folded to increase its

   surface area and provide more room for electron

   transport chain

   --each contains three large protein complexes with

     carrier molecules and associated enzymes

   --have a small protein called cytochrome c

   --and nonprotein component called ubiquinone (Q)

---critical thinking time, why is preparatory Krebs and

   Krebs cycle located within the matrix?

16. Summarize the net ATP yield from the oxidation of a glucose molecule by constructing an ATP ledger that includes coenzyme production during the different stages of glycolysis and cellular respiration.

---glycolysis: 2 ATP (net) and 2 NADH

---preparatory Krebs: 2 NADH

---Krebs cycle: 2 ATP; 6 NADH; 2 FADH2

---Totals (net): 4 ATP; 10 NADH; 2 FADH2

17. Describe the fate of pyruvate in the absence of oxygen.

---if oxygen supply to a respiring cell is cut off and the

   cell has no other metabolic pathway available to it, it

   will die

---many cells can switch to fermentation

   --some cells do only fermentation

---when fermenting, ATP needs come solely from glycolysis

   --glycolysis produces 2 ATP (net); 2 NADH, and 2 three-

     carbon molecules called pyruvate

---NAD+ is required for fermentation and it is reduced to


   --fermenting cell must figure out some way to regenerate

     NAD+ or glycolysis will shut down

---and what to do with all that pyruvate which is

   technically “useless?”

---**use the pyruvate to regenerate the required NAD+

---using pyruvate as oxidizing agent for NADH results in

   changing it into something else

---key concept: some organisms choose to ferment even in

   presence of oxygen

---**some do anaerobic respiration by using an inorganic

   molecule other than oxygen as final electron acceptor

   --nitrate to nitrite

18. Explain why fermentation is necessary.

---fermentation allows glycolysis to produce a SMALL but

   SUSTAINED amount of ATP

   --only as much is produced as can be obtained from

     substrate-level phosphorylation

---glycolysis rate increases 10 fold to produce needed


---fermentation will allow some cells lacking oxygen to

   perform needed functions

---“aerobic” cells cannot ferment indefinitely



19. Contrast the products of lactic acid fermentation and alcoholic fermentation.

---lactic acid fermentation reduces pyruvate to lactate

   --uses NADH as reducing agent

---3 carbon pyruvate changed into 3 carbon lactate

---human muscle cells can ferment if need be but not

   neurons or cardiac muscle cells

   --what makes one’s muscle sore

---eventually lactate converted to pyruvate and “burned”

   in process of paying “oxygen debt”

---certain yeasts and some plant cells perform alcoholic


---this process requires two enzymes to metabolize pyruvate

---one enzyme removes a carbon dioxide from pyruvate

   leaving acetaldehyde

---acetaldehyde reduced by NADH producing NAD+ and

   ethyl alcohol (ethanol)

---where would we be without bread and booze?

---should be aware that some microorganism produce widely

   different acids and end products from two discussed

20. Contrast the energy yield of aerobic respiration and fermentation.

---aerobic respiration can produce 36-38 ATP per glucose

   --depends on organism and type of cell

---anaerobic respiration can produce equivalent amounts of


---fermentation produces only 2 ATP (net) per glucose via



Biology 101 Chapter 7

Student Self Assessment Short Answer


1.  Part of the unusually large amount of free energy that results from the hydrolysis of ATP derives from the large number of _________ charges near each other on neighboring phosphate groups.


2.  Oxidation and ________________ occur together.


3.  The chemiosmotic formation of ATP during the operation of the respiratory chain is called ___________________________  ____________________________.


4.  The loss of an electron by a ferrous ion (Fe2+) to give a ferric ion (Fe3+) is called _________________________.


5.  In a redox reaction, the reactant that becomes oxidized is called a __________________  _______________________.


6.  The conversion of glucose to lactic acid is a form of _____________________.


7.  Fatty acids must be converted to ____________  _______ before they can be used for respiratory ATP production.


8.  Thanks to its ability to carry electrons and free energy, _____________ is the major universal energy intermediary in cells.


9.  During alcohol fermentation, NAD+ is regenerated by the reduction of acetaldehyde to ___________________________.


10. The earliest forms of life probably used ________________________ to generate ATP.



Biology 101 Chapter 7

Student Self Assessment Multiple Choice


____1.  During respiration, NADH donates two electrons to ubiquinone.  When this happens, ubiquinone is _____________.

     a. reduced                         b. oxidized

     c. phosphorylated            d. hydrolyzed


____2.  Isocitrate dehydrogenase is an enzyme of the citric acid cycle.  Where in the cell is this enzyme located?

     a. in the thylakoids           b. in the cytoplasm

     c. in the mitochondrial matrix     d. in the chloroplast


____3.  The oxidation of pyruvate to carbon dioxide is called ____.

     a. fermentation                   b. the citric acid cycle

     c. glycolysis                 d. oxidative phosphorylation


____4.  The oxidizing agent at the end of the respiratory chain is __.

     a. O2                            b. NAD+

     c. ATP                        d. FAD


____5.  According to the chemiosmotic theory, the energy for the synthesis of ATP during the flow of electrons down the respiratory chain is provided directly by the __________.

     a. hydrolysis of GTP               b. reduction of NAD+

     c. diffusion of protons      d. reduction of FAD


____6.  The portion of aerobic respiration that produces the most ATP per mole of glucose is _____________________________.

     a. oxidative phosphorylation b. the citric acid cycle

     c. glycolysis                 d. lactic acid fermentation


____7.  The site of oxygen utilization is the ______.

     a. nucleus                         b. chloroplasts

     c. endoplasmic reticulum       d. mitochondria


____8.  When yeast cells are switched from aerobic to anaerobic growth conditions, the rate of glycolysis increases.  The rate of glycolysis is regulated by the concentration of _______.

     a. ATP                        b. acetyl CoA

     c. oxaloacetate                   d. FAD


____9.  In human muscle cells, the fermentation process produces ___.

     a. lactic acid                 b. 12 moles of ATP

     c. pyruvic acid                 d. an excessive amount of energy


___10. The chemiosmotic generation of ATP is driven by ____.

     a. osmotic movement of water into an area of high solute


     b. the addition of protons to ADP and phosphate via enzymes

     c. oxidative phosphorylation

     d. a difference in H+ concentration across a membrane

Biology 101 Chapter 8

Photosynthesis: Energy from the Sun



1.  Write and describe a balanced equation for photosynthesis.

---6 CO2 + 6 H2O ----> C6H12O6 + 6 O2

   --not quite right, but close enough

---chalk talk time on photosynthesis equation

---light and chlorophyll omitted from above equation but


---conversion of light energy into chemical energy

---conversion of inorganic substances into organic


2.  List and briefly describe the two pathways involved in photosynthesis.

---photosynthesis occurs in chloroplasts of photosynthetic


---light reactions and dark reactions

   --light reactions are aptly named

   --dark reactions are a misnomer

---light reactions require the presence of light

   --used to say sunlight but can buy grow bulbs

---dark reactions CAN AND DO run in presence of light but

   NOT depend on the light per sec

   --dependent on products of light reaction  

---light reactions driven by light energy and produces

   ATP and reduced electron carrier (NADPH + H+)

---dark reaction (Calvin-Benson cycle) does not use

   light directly; uses ATP, NADPH + H+, and CO2, to

   produce sugar

3.  Explain the role of redox reactions in photosynthesis.

---light reaction composed of two photosystems

   --PSI and PSII

   --can run either cyclic or noncyclic electron flow

---light reactions are series of redox reactions using

   electron carriers in thylakoid membrane and


---depending on what is “running” can make ATP and NADPH

4. Briefly describe how a photon may excite an electron to a higher energy level.

---light is a form of electromagnetic radiation

---wave-theory explains most of what we know about light

---the waves are composed of discrete packets of energy

   called photons

---wavelength of light is distance from the peak of one

   wave to the peak of the next wave

---humans see light in range of wavelengths from 400 to

   700 nm

--immediately below 400 is ultraviolet; immediately above

  700 is infrared

---**shorter the wavelength, the greater the energy

---energy is inversely proportional to wavelength

---intensity (brightness) of light at given point is the

   amount of energy falling on a given area

---three things can happen when photon meets a molecule

   --may bounce off (be reflected)

   --may pass through (be transmitted)

   --**may be absorbed by the molecule

---if photon is absorbed, it disappears but not its energy

---when molecule absorbed a proton, it acquires the energy

   of that photon

---it is raised from a ground state to an excited state

---increase in energy boosts one of its electrons into

   orbital farther from nucleus

   --may fall back down and release that energy as light

   --may be excited and lost to the molecule

---molecules that absorb wavelengths in visible spectrum

   are called pigments

---let’s talk a moment about reflection and absorption

5.  Explain why the absorption spectrum for chlorophyll differs from the action spectrum for photosynthesis.

---in plants, two chlorophylls predominate

   --a and b

---chlorophylls absorb blue and red wavelengths (their

   action spectrum)

---if only the chlorophyll pigments were active in

   photosynthesis, much of visible spectrum would be unused

---all photosynthetic organisms possess accessory pigments

   which absorb photons between red and blue wavelengths

   and transfer that energy to the chlorophylls

---carotenoids and phycobolins

6.  List the wavelengths of light that are most effective for photosynthesis.

---see #5 above

---red and blue

7.  List the pigments involved in photosynthesis.

---chlorophyll a and chlorophyll b

---carotenoids (β-carotene and others) absorb photons in

   blue and blue-green wavelengths and appear deep yellow

---phycobolins (phycoerythrin and phycocyanin) absorb in

   yellow-green, yellow, and orange wavelengths



8.  Explain what happens when chlorophyll or accessory pigments absorb photons.

---when pigment molecule absorbs photon and becomes excited

   it can return to ground state emitting much of absorbed

   energy as fluorescence or the molecule passes some of

   the absorbed energy to another pigment molecule

---pigments are arranged into energy-absorbing antenna


   --excitation passes from one pigment molecule to another

       until reaches the reaction center

   --reaction center is always chlorophyll a molecule that

     absorbs longest wavelengths

---light energy absorbed is passed along as an electron

---ground state chlorophyll (Chl) is not much of a

   reducing agent, but excited chlorophyll (Chl*) is

   --Chl* can react with an oxidizing agent

---**electron(s) can be boosted out of photosystem

   beginning series of redox reactions (chemiosmosis)

9.  Describe what happens to electrons when chlorophyll is reduced and how this energy is used to make ATP via photophosphorylation.

---chalk talk time with PS I and cyclic electron flow

10. List the components of a photosystem and explain their function.

---photosystem is accumulation of pigment molecules held

   together by series of proteins in right orientation

   for light absorption

---pigment molecules located so they can pass the

   excitation to next pigment molecule in the system

---eventually winds up at reaction center which (in plants)

   is a chlorophyll a molecule

   --absorbs at the highest wavelength of all pigments in


---reaction center can “boost” an electron out of

   photosystem to electron carriers in electron transport

   chain in thylakoid membrane

11. Trace noncyclic electron flow through photosystems I and II.

---chalk talk time with noncyclic electron flow

---PSI loses electrons that wind up in NADPH

   --would soon run out of electrons and reaction would


---PSII’s excited electrons used in chemiosmosis to make


   --electrons then cycle into PSI so it can keep running

     and making NADPH


---PSII in danger of running out of electrons and would

   have to shut down

---PSII replaces its lost electrons by splitting water

   --2 electrons, 2 H+’s and 1 oxygen atom (1/2 O2)

12. List the products of photosystems I and II.

---PSI in cyclic electron flow can make ATP by chemiosmosis

   --ATP coin of the realm, why is PSII even needed?

---noncyclic electron flow using PSI and PSII has PSI

   making NADPH and PSII making ATP, H+, and oxygen  

13. Highlight the reactants and products of the light reactions and describe where they occur using the balanced

equation for photosynthesis.

---6 CO2 + 6 H2O ----> C6H12O6 + 6 O2

---water molecules needed in noncyclic electron flow for

   splitting to replace lost electrons from PSII

---diatomic oxygen produced during light reactions

   --two water molecules split --> one diatomic oxygen

---what is NOT shown by balanced formula are the NADPH’s

   and ATP’s that are made for consumption in the dark


   --we will discover that it takes 12 NADPH and 18 ATP

     to “fix” one glucose molecule

14. Describe important similarities and differences in chemiosmosis between oxidative phosphorylation in mitochondria and photophosphorylation in chloroplasts.

---chemiosmotic mechanisms works in both oxidative and


---in chloroplasts, as in mitochondria, electrons move

   through series of redox reactions, releasing energy,

   which is used to transport protons (H+) across a


---this active proton transport = proton-motive force

   --difference in pH and electric charge across membrane

---in mitochondrion, protons pumped out of matrix, across

   inner membrane, into space between inner & outer


---in chloroplast, protons pumped into interior of

   thylakoid (from stroma into interior of thylakoid)

---electrons diffuse through specific channel proteins

   (ATP synthease) that couples formation of ATP to

   diffusion of protons back across membrane

15. Summarize the function of the Calvin-Benson cycle.

---often called the “dark reactions”

---reactions of this pathway incorporate CO2 into sugar

---Calvin-Benson cycle occurs in the stroma of chloroplast



---cycle so “something” must already be there for cycle

   to run on

16. List and briefly describe the three processes that comprise the Calvin-Benson cycle.

---cycle uses high-energy compounds made during light

   reactions to reduce CO2 to carbohydrate

---are three processes that make up the cycle


---RuBP (ribulose 1,5 bisphosphate) already present in

   stroma and is compound that begins “cycle”

   --5 carbon compound with two phosphates

---rubisco “fixes” carbon from CO2 into RuBP

---forms unstable 6 carbon bisphosphate molecule-->splits

   into two 3-carbon phosphated molecules (PGA)


---series of reactions involves phosphorylation using

   ATP made in light reactions and a reduction using

   NADPH made in light reactions

---product of interest is G3P (sometimes called PGAL)

---two G3P can be combined to make one glucose

---in typical leaf, about 1/3 of G3P winds up in starch

---two thirds of G3P product is converted to sucrose

   --transported out to other organs where hydrolyzed to

     glucose and fructose for various uses

---carbons from glucose used to make amino acids, lipids,

   and building blocks of nucleic acids

---just how important is this process?


---most of G3P ends up as regenerated RuBP so cycle can


---for every turn of cycle, with one CO2 fixed, the acceptor

   gets regenerated

---**takes 6 turns of cycle to make one glucose molecule

17. Describe the role of ATP and NADPH in the Calvin cycle.

---12 ATP required to change 12 3-phosphoglyceric acid to

   12 1,3 bisphosphoglyceric acid (diphosphoglyceric acid)

---12 NADPH required to finish conversion of 1,3

   diphosphoglyceric acid to G3P

---2 of the 12 G3P converted to one glucose

---other 10 are converted to 6 ribulose 5-phosphate

---requires another 6 ATP to convert ribulose 5-phosphate

   into RuBP so cycle can continue

18. Describe the fate of each reactant and the method of production for each product using the balanced equation for photosynthesis.

---balanced formula already provided and should be known!

---CO2 is “fixed” into G3P; 2 GP3 = one glucose

---H2O used to provide electrons for PS II during noncyclic

   electron flow; some protons (H+) from splitting of water

   wind up in the carbohydrate; O2 made by splitting of

   water is released to environment

19. Describe the fate of photosynthetic products.

---glucose produced used by plant to make other compounds

   beside sugars

   --amino acids, lipids, precursors of nucleic acids

---much of stored energy in these products released by\

   glycolysis and cellular respiration during plant growth,

   development, and reproduction

---much plant matter ends up being consumed by animals

   --glycolysis and cellular respiration in animals

     releases free energy from plant matter for use in

     animal cells


Biology 101 Chapter 8

Student Self Assessment Short Answer


1.  During cyclic photophosphorylation, the energy of photons is converted to the chemical energy of the product, __________________________.


2.  In both photosynthesis and respiration, ______________ synthesis is coupled to the diffusion of protons across a membrane.


3.  The Calvin-Benson cycle is sometimes called the _______________________  ____________________________.


4.  The oxygen found in the Earth’s atmosphere is generated from photosystem ______________________________ of noncyclic photophosphorylation.


5.  The most abundant enzyme in the biosphere is __________________________.


6.  During the light reactions of photosynthesis, the synthesis of ___________________ is coupled to the diffusion of protons.


7.  When ________  __________________ are exposed to light and CO2, four-carbon compounds are the first carbon-containing products.


8.  In noncyclic photophosphorylation, the electrons for the reduction of chlorophyll in photosystem II come from _____________________________.


9.  Atmospheric carbon dioxide enters plants through openings called ___________________________.


10.  During the process of _____________________, rubisco catalyzes the reaction of RuBP with oxygen.



Biology 101 Chapter 8

Student Self Assessment Multiple Choice


____1.  A molecule has an absorption spectrum that shows maximum absorption within the wavelengths of visible light.  This molecule is _________.

     a. a reducing agent           b. a quantum

     c. a photon                     d. a pigment


____2.  Photophosphorylation provides the Calvin-Benson cycle with __.

     a. protons and electrons       b. CO2 and water

     c. ATP and NADPH                d. ground state chlorophyll


____3.  The enzyme rubisco is found in ______.

     a. chloroplasts                   b. mitochondria

     c. the cytoplasm                  d. the nucleus


____4.  The NADPH required for the reduction of 3PG to G3P comes from the _______.

     a. dark reactions            b. light reactions

     c. synthesis of ATP               d. Calvin-Benson cycle


____5.  In both photosynthesis and respiration, protons are pumped across a membrane during ______.

     a. electron transport            b. photolysis

     c. reduction of oxygen       d. glycolysis


____6.  Based on its electron structure, a molecule has a range of photon energies.  These photon energies are known as the molecule’s ________.

     a. chlroplasts                    b. light reactions

     c. absorption spectrum        d. photosystem I and II


____7.  Heterotrophs are dependent on autotrophs for their food supply.  Autotrophs can make their own food by _____.

     a. feeding on bacteria and converting the nutrients into usable


     b. using light and an inorganic carbon source to make reduced

        carbon compounds

     c. synthesizing it from water and carbon dioxide

     d. recycling the decomposing bodies of dead organisms


____8. If one were to compare long wavelengths to short wavelengths, it would be evident that short-wavelength photons have _____.

     a. an insignificant amount of energy

     b. more energy

     c. energy not available to plant cells

     d. a ladder of energy


____9.  In cacti, CO2 is stored for use in the Calvin-Benson cycle ___.

     a. in the stems, roots, and leaves     b. during the evening

     c. in glucose molecules            d. in the stroma