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Chapter 2: Water and Carbon—The Chemical Basis of Life
Lecture 2 PPT Review:
1.) What is electronegativity? Compare and contrast polar covalent vs nonpolar covalent bonds?
a. Electronegativity = A measure of the ability of an atom to attract electrons toward
itself from an atom to which it is bonded (caused by number of protons in NUC and
distance between NUC and valence shell.
b. Nonpolar Covalent—electrons are shared equally between atoms of the same or
similar electronegativity
Polar Covalent—electrons are shared unequally between atoms differing in
electronegativity. This results in a the more electronegative atom having a partial
negative charge and the other atom having a partial positive charge
2.) Why do partial charges form on molecules?
^^^
3.) What is an ionic bond?
a. Electron is completely transferred from one atom to another so that the atoms remain
associated due to their opposite electric charges
4.) Explain the properties of water
a. Polar or Nonpolar?
i. Polar
b. Covalent or noncovalent bonding?
i. Covalent
c. Partial charges for each atom?
i. Partial negative on oxygen and partial positive on H’s
5.) What types of bonds form between water molecules?
a. Hydrogen bonds
6.) Why is water an excellent solvent? (p.25) –think about its interaction with an ionic molecule like
NaCl.
a. Electronegativity causing partial + and partial – charge
b. Molecule is bentPartial – charge of O sticks out, away from the partial + charges on
H. Makes it so these partial charges can interact with those on other H2O (H-bonding)
or other molecules.
i. Ions and polar molecules stay in solution bc of their interaction w/ H2O
charges
7.) Are nonpolar molecules hydrophilic or hydrophobic? What properties of both the molecule and
water cause this?
a. HydrophobicUncharged and nonpolar. They have minimal or nonexistent
interaction with water. H2O is opposite of this (Polar w/ the partial charges)
8.) What are the two properties of buffers we discussed?
1. Resist changes in pH
2. Have the ability to accept or donate H+
9.) What is pH? What is the physiological pH?
a. pH = the concentration of H+ (proton) in solution
b. Physiological pH = 6.5 – 8.0
10.) At a basic pH, what is the relationship between [OH-] and [H+]? What is the relationship at an
acidic pH?
a. Basic = [OH-] > [H+]
b. Acidic = [H+] > [OH-]
11.) What types of bonds can carbon form? How many?
a. Covalent bonds
b. 4 because Carbon has 4 electrons in outer valence shell so needs 4 more electrons to
complete octet. Therefore forms 4 covalent bonds to satisfy this.
12.) Be sure to know the functional groups and family of molecules that Dr. A recommended to
know!
13.) Review the examples on the PPT + Bioskills 6 and 8 in Appendix B of textbook.
Chapter 3: Protein Structure and Function
Lecture 3 “PSF” Review:
1.) What is an amino acid (AA)? What are the structural components of an AA? What is the central
carbon denoted as?
a. AA = the building blocks of proteins, each containing an amino group, a carboxylic
group, and a side chain (R group) attached to the alpha carbon
2.) What is the difference between the non-ionized form of an AA and the ionized form? (Be able to
draw both is a good idea!)
a. Ionized has carboxylic group deprotonated (COO-) and amino group protonated
(NH3+)
3.) Why do AAs ionize at pH 7?
a. Water has a pH of 7—“the concentration of protons at this pH causes the amino group
to act as a base, and it attracts a proton to form NH3+ -- Carboxyl group acts as an acid
and the EN oxygen atoms pull the electron away from its hydrogen making it easy to
lose the proton
4.) Which structural component of an AA distinguishes it from all of the other AAs?
a. The side chain (R group)
5.) Classify the AAs according to the following properties of their side chains:
a. Nonpolar
i. G A P I L V M C F W
b. Polar
i. S T Y N Q
c. Polar (+) charge
i. H R K
d. Polar (-) charge
i. D E
6.) Which AAs are basic? Which are acidic?
a. Basic = H R K
b. Acidic = D E
7.) What is the name of the covalent bond that links peptides? What reaction joins peptides
together? What molecule is released during this reaction? What is the reverse of this reaction?
a. Peptide Bond
b. Condensation Rxn
c. H2O released
d. Hydrolysis
8.) Is the directionality of AA arranged CN terminus or NC terminus?
a. NC
9.) Describe the flexibility of the peptide backbone. Why is this an important concept for protein
formation?
a. Peptide bond has partial double bond character which limits free rotationthe bonds
directly adjacent to the alpha carbon have some rotation
b. Limited rotation will only allow certain conformations possible
10.) Explain the four levels of protein structure.
a. 1* = sequence of amino acids
b. 2* = Hydrogen bonding between peptide backbone that form alpha helices and beta
sheets. H-bonding between C=O on one AA to the Hydrogen on N-H of another AA
c. 3* = Interactions between the R groups causes the protein to adopt its folded
structure. One of the driving forces here is the hydrophobic effect. Disulfide bridges
between Cys, van der waals/electrostatic interactions, h-bonding between 2 side
chains + between a side chain and the backbone, and ionic bonding also contribute.
d. 4* = Multiple polypeptides coming together to form a single structure. Can have
different functions. Defined by “domains” of the protein
11.) After studying the levels of protein structure and the interactions that cause each, be sure to
understand the example of hemoglobin and how a single AA change will alter its function
(p.84)
12.) How does the arrangement of alpha-helices vs beta-sheets affect which residues will interact
with one another? (Think about how they’re arranged in the primary structure + how each 2nd
structure is arranged)—(p.85)
a. Alpha helices can form h-bonds that are 4 positions (in primary structure) apart vs
beta sheets can form h-bonds between residues that may be 100 or more residues
apart (in primary structure) depending on the length of each sheet/turn
13.) Are peptide bonds broken when proteins denature? What two ways (that we discussed) can a
protein be denatured?
a. Peptide bond stays intact
b. Heat and surface denaturation
Chapter 4: Nucleic Acids and the RNA World
Lecture 4 PPT Review:
1.) What are the structural components of nucleic acids? Nucleic acids are also referred to as what
type of molecule?
a. 5-carbon sugar, nitrogenous base, and phosphate group
b. Nucleotide
2.) What structural feature distinguishes ribose from deoxyribose?
a. Ribose has OH on C2 while deoxyribose has H on C2
3.) What are the names of all the nitrogenous bases? Which are purines and which are pyrimidines?
What general structural characteristic distinguishes purines from pyrimidines?
a. Adenine, Guanine, Cytosine, Thymine, Uracil
b. A and G = purines, C, T, U = pyrimidines
c. A and G are larger—they have the extra 5C cyclic ring attached.
4.) How do DNA and RNA differ in:
a. Function
i. DNA stores genetic info
ii. RNA has many fxns and structures
b. Composition
i. Deoxyribose vs ribose
5.) What reaction joins nucleotides in a DNA and RNA chain? What is the name of the bond that
forms? What molecule is released from this reaction? What components of the nucleotide are
interacting in this reaction?
a. Polymerization (condensation) rxn.
b. Phosphodiester linkage (bond)
c. H2O released (condensation)
d. Phosphate OH attached to C5 on one nucleotide with OH attached to C3 of
nitrogenous base of another nucleotide
6.) What two interactions are occurring in the DNA double helix? Explain each. Together, both yield
what structural benefit for the helix?
a. Complementary base pairing and Base stacking by hydrophobic interactions
b. Provides stability
7.) The directionality of the nucleotide sequence is read in what direction? Why?
a. 5’  3’ (because of phosphodiester linkage between 5’C of one nuc with 3’C of
another nuc.  one end of the sugar-phosphate backbone has an unlinked 5’
phosphate while the other end has an unlinked hydroxyl
8.) How many bonds form between Guanine and cytosine versus adenine and thymine? How does
heat denaturation affect these bonds? Therefore, how would you expect the composition of G’s
and C’s vs A’s to T’s to differ in the DNA of an organism that lives in very high temperatures
versus low temperatures?
a. 3 H bonds between G---C | 2 H bonds between A and T
b. Heat denaturation breaks H bonds
c. A higher concentration of G---C would provide the most stability against heat
denaturation
9.) What are the general steps in DNA synthesis? What catalyzes polymerization in cells?
a. Strand separation
b. Base-pairing
c. Polymerization---Catalyzed by DNA polymerase
10.) How does the secondary structure of RNA differ from that of DNA? What about tertiary
structure?
a. RNA has hairpin loop + helices. DNA has beta sheets and alpha helices
b. RNA can form tertiary. DNA has no tertiary structure
11.) What are the major types of RNA?
a. Ribosomal
b. Messenger
c. Transfer
d. Small nuclear
e. Micro
12.) What protein enzyme catalyzes splicing of introns in “precursor” rRNA? What did this discovery
indicate?
a. RNA is catalytic—ribozyme
13.) What is the function of most ribozymes? What do rRNA catalyze during translation?
a. Most catalyze the breaking of phosphodiester bonds
b. During translation, rRNA catalyzes formation of peptide bonds
14.) What are the components of the RNA World Hypothesis?
a. RNA replicates itself
b. Self-replicating RNA also catalyzes protein synthesis
c. DNA becomes the genetic material and codes for RNA
Lecture 6: Introduction to Carbohydrates
Lecture PPT Review:
1.) What is a monosaccharide? What is the general formula for a monosaccharide? What bond
allows monosaccharides to form polysaccharides?
a. Monosaccharide = molecule that has molecular formula (CH2O)n and cannot be
hydrolyzed to form any smaller carbs
b. Forms polysaccharides via glycosidic linkages
2.) Understand the general structure of CHOs (Fischer projection is usually easier to
remember/recognize than Haworth projections) and how a difference like the one in glucose
vs galactose changes the molecule and how each might form.
3.) What do the functional groups tell you about the properties of monosaccharides? (3 discussed
in lecture)
4.)
5.)
6.)
7.)
a. Polar
b. Hydrophilic
c. Forms Hydrogen bonds
What is the structural difference between
a. Aldose and ketose
i. Aldose has carbonyl at end of chain/Ketose has carbonyl in middle of chain
b. Glucose and galactose
i. Differ only by positioning of one hydroxyl OH on C4
Review ring structure conformation of sugar using α- and β-glucose example. Why do sugars
tend to adopt the ring structure?
a. More stable in ring structures—which is favorabletherefore occurs spontaneously
How are disaccharides formed? How does the structure of fructose differ from glucose?
a. Condensation Rxn
b. Fructose is 5C ring
Complete the following reaction:
a. Gives you fructose and glucose
8.) What is the role of glycoproteins in cell identity?
a. Each cell in your body has glycoproteins on its surface that identify it as part of your
body (important for immune system!)—Keep in mind that there are huge potential for
oligosaccharides to be unique, therefore each cell type and species can display a
unique identity
9.) What are two of the major roles of polysaccharides discussed in class?
a. Energy storage depots
b. Structural scaffolds
10.) Compare/contrast the types of polysaccharides by each of the following:
a. Roles/Uses
b. Glycosidic Linkage/Chemical Structure
c. 3D structure
d. Use table 5.1 in book to review this
11.) Difference between Amylose and Amylopectin?
a. Amylose has unbranched helices while amylopectin has branched helices
12.) Explain the role of carbohydrates in chemical energy storage.
a. Starch and glycogen can convert glucose to ATP
13.) What feature makes cellulose, chitin, and peptidoglycan advantageous for organismal
structures? Explain why.
a. The beta1,4 glycosidic linkages are 1.) difficult to hydrolyze and 2.) very few enzymes
have active sites that accommodate their geometry
Lecture 7/8 Lipids and Cell Membrane
Lecture PPT Review:
1.) Describe the solubility of lipids.
a. Insoluble or only slightly soluble in H2O
2.) What are the general structural components that form triglycerides? Draw the general structure
of a triglyceride.
a. Glycerol w/ ester linkages attaching 3 fatty acid tails (hydrocarbon chains)
3.) What attributes determine the properties of FAs? Compare and contrast saturated vs
unsaturated fats at room temperature (that we discussed in lecture—think back to video).
a. SaturatedNo double bonds, linear structure, high melting point, solid at RT, “fat”
b. Unsaturated  double bonds, kink in structure, low melting point, liquid at RT, “oil”
4.) Why are phospholipids structurally important for eukaryotes? What are the structural
components? Describe the hydrophobicity of these components.
a. Essential for cell membrane—serving as barrier to outside world
b. Amphipathichas polar/charged group bound to a phosphate and linked to a glycerol
molecule via phosphodiester linkage = hydrophilic head (interacts with surrounding
H2O) and hydrophobic FA tail(s)
5.) What is selective permeability? What two characteristics of a molecule is permeability
dependent on? Arrange the following in terms of highest to lowest permeability:
a. CO2
f. O2
b. Na+
g. Glycerol
c. Sucrose
h. H2O
d. N2
i. K+
e. Clj. Glucose
-
O2, CO2, N2 > H2O, Glycerol > Glucose, Sucrose > Cl-, K+, Na+
Permeability is dependent on temperature and fluidity (think—what is the composition of
the membrane fats?)
6.) What is the net water movement via osmosis under the following conditions? Describe the
outcome/appearance for a RBC under these conditions, as well.
a. Isotonic Solution – relative solute concentration is at equilibrium between inside and
outside of cell—normal cell morphology
b. Hypertonic Solution – high relative solute concentration outside of cell-->H2O moves
more freely out of the cell into ECM—causing cell to shrivel up/shrink
c. Hypotonic Solution – high relative solute concentration inside the cell-->H2O will
move more freely into the cell than out of the cell—causing cell to swell
7.) What is facilitated diffusion? How are ions passing through the membrane? (think
concentration gradient) Does this transport require energy? What are allosteric proteins? What
example was used in class to supplement this?
a. Specific molecule binds to carrier protein in the membranewhich causes
CCcausing molecule to travel down concentration gradient (so no energy required).
Going from high concentration to low concentration**
b. Allosteric proteins undergo shape change caused by binding (or other interaction)
with another molecule/protein
c. GLUT1 protein example
8.) What is active transport? How are ions passing through the membrane? (think concentration
gradient) Does this transport require energy? What example was used in class to supplement
this?
a. Transporting molecules from low concentration to high concentration (against
concentration gradient) therefore energy from ATP input is required. ATP hydrolysis
and molecule-binding cause carrier protein to change shape (conformational change)
and the CC then allows the molecule to be released into the new environment
b. Sodium-Potassium pump was example in class
9.) Permeability is a function of what two parameters? How does the molecular structure of the
phospholipid bilayer influence these?
a. Temperature and fluidity
b. Short and unsaturated lipid bilayer = higher permeability and fluidity
c. Long and saturated lipid bilayer = lower permeability and fluidity
10.) What structural component of steroids distinguishes these lipids from others? What example
from lecture did we discuss? What 2 functions did we discuss this example as having?
a. The four cyclic rings
b. Cholesterol—cell membrane component and precursor of vitamin D and sex steroid
hormones
11.) Be sure to know the basics of the different membrane proteins that facilitate transport (both
facilitated diff. and active transport)
12.) Review transport animations
Lecture 9 Energy and Enzymes: An Introduction to Metabolic Pathways
Lecture 9 PPT Review:
1.) What is the 1st law of thermodynamics?
a. States that energy can be transferred and converted into different forms, but it cannot
be destroyed
2.) Explain potential and kinetic energy—using one of the examples from class may be a good way
to practice this.
a. Potential energy is energy associated with position or configuration—stored energy
b. Kinetic energy is energy of motion
c. In the waterfall example from class: A water molecule at the top of a molecule has
high potential energythen as it falls the energy is converted to kinetic energyonce
it strikes the rocks at the bottom, the kinetic-motion energy is converted to other
kinds of energy (included mechanical, heat, sound)
3.) What is the second law of thermodynamics? Where is potential energy stored in a molecule?
a. Second law states that entropy will always increase in an isolated system
b. Potential energy is stored in the chemical bonds of a molecule
4.) If a reaction is favorable in the direction of reactantsproducts:
a. Which would have the highest potential energy?
i. Reactants
b. Would the entropy be high or low in the High PE component?
i. Low entropy (More ordered)
5.) What is a redox reaction? What is oxidation? What is reduction? Is oxygen usually an e- acceptor
or donor?
a. Redox rxn = a chemical reaction that involves the loss or gain of one or more electrons
b. Oxidation is the loss of electrons
c. Reduction is the gain of electrons
d. Oxygen is usually the electron acceptor
6.) Arrange the following bonds in terms of increasing potential energy: N-H | C-H | O-H
a. O-H (lowest PE) --> N-H --> (highest PE)
7.) Define:
a. Exothermic reaction
i. A chemical reaction that can occur spontaneously, releasing heat and/or
increasing entropy, and for which the Gibbs free energy is less than zero
b. Endothermic reaction
i. Chemical reaction that requires an input of energy to occur and for which the
Gibbs free energy is greater than zero.
8.) Why are endergonic reactions linked to exergonic reactions in cells? –> So why is ATP hydrolysis
an important reaction in cellular energetics?
a. Endergonic reactions require an input of energy—Exergonic reactions release energy.
Therefore, the energy released by the exergonic reaction can be used to drive the
endergonic reaction forward
b. ATP hydrolysis releases high amount of energy and can initiate many of the cell’s
endergonic reactions
9.) What structural component of ATP causes it to have potential energy stored within the
molecule?
a. The triphosphate component has the (-) charges of each phosphate in close proximity.
Since like charges repel each other, this makes hydrolysis very favorable (exergonic) to
relieve the repulsion between the (-) charges
10.) What is the activation energy of a reaction? How do molecules deal with this?
a. The amount of energy required to initiate a chemical reaction; specifically, the energy
required to reach the transition state
b. Energy molecules must collide in precise orientation and overcome mutual
repulsion—enzymes help to lower the activation energy
11.) Define:
a. Enzyme
i. A globular protein that is specialized to serve as a catalyst
b. Catalyst
i. A substance that lowers the energy of activation for a reaction by forming a
temporary association with the reacting molecule
12.) Draw the generic energy profile include:
a. Reactants
b. Transition State
c. Products
d. Label the x and y axis
e. State whether your rxn is exergonic or endergonic
f. Ea
g. ΔG