BIOSC 0150 Dr.

Ahn

MODULE 1 EXAM REVIEW

NOTE: This is a Module 1 review for you to use as another resource in your studying. By no
means is this a comprehensive review of everything you may be expected to know for the exam,
but this review will cover many major concepts. Similarly, not everything on this guide will show
up on the exam. It is set up with a summary of content from the lectures in addition to
embedded questions related to each of the topics (most of them open-ended) to encourage you
to use active recall and apply your knowledge so that it helps you figure out where to focus your
studying. You will find that the material summarized lines up with the lecture slides in the order
they were presented so that you can easily refer back to the slides as you see fit. An answer key
will be posted later in the week so that you have time to work through the questions on your
own or get help. Feel free to reach out to any of us as you prepare for the exam; we are here to
help you! Good luck and happy studying :)

Lecture 1.1
Living organisms share some common characteristics. (1) What are these characteristics?

Lecture 1.2
General Atomic Structure
- Atoms have protons (+) and neutrons in the nucleus and electrons (-) in “shells” around
the nucleus
- The number of protons in an atom is the atomic number
- Electrons in the outermost shell of an atom are called valence electrons and help
determine the bonding and chemical properties of the atom
- 6 elements that make up a majority of living matter: C, H, N, O, P, S
- Chemistry of life is organized around the carbon atom because it is versatile in its
bonding (can form single, double, or triple bonds and can bond to a variety of
other atoms)

(2) Define an isotope and give an example if you can.

(3) What is the atomic number of magnesium?

(4) How many protons and electrons does the sulfide ion have (S2-)?

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Chemical Bonding
- Covalent bond: strong, stable bonds that occur when two atoms share electron pair(s) –
require a large input of energy to break
- Can be polar or nonpolar – this is determined based on the electronegativity of
the two atoms involved in the bond
- Electronegativity depends on the number of protons in the nucleus and
the size of the atom (distance between nucleus and valence shell)
- Greater electronegativity = more strongly able to attract electrons
- Polar covalent bond: occurs when two atoms share electrons unequally → results in a
molecule where certain atom(s) may have a partial positive or partial negative charge
- Electronegativity hierarchy: O > N > C ≅ H
- Nonpolar covalent bond: occurs when two atoms share electrons equally or nearly
equally
- Ionic bond: occur as a result of the transfer of electrons between oppositely charged
ions (this transfer of electrons usually leads to both atoms having a charge but being
stable because they have full valence shells)
- Hydrogen bond: weak attraction that occurs between an electronegative atom and a
hydrogen bonded to another electronegative atom
- A helpful way to think about and understand hydrogen bonding:
- Hydrogens bonds are attractions that occur between two molecules and
NOT within a molecule
- The attraction is very specific: it occurs because the partial positive charge
on a hydrogen atom is able to attract to the partial negative charge on
another electronegative atom – this is why the hydrogen MUST also be
polar covalently bonded to an electronegative atom
- See Canvas discussion board for a visual diagram and a lengthier
explanation of hydrogen bonding if you are still confused
- Hydrophobic interactions: bring together nonpolar molecules when they are in the
presence of a polar substance (since the nonpolar molecules don’t want to interact with
a polar substance, they tend to aggregate with each other to minimize their interactions
with the polar substance

Water
- Water has unique properties due to its structure, which allows it hydrogen bond well
- Ice is less dense than liquid water because of differences in hydrogen bonding
- In ice, water is held in a rigid structure by hydrogen bonds
- In water, hydrogen bonds continually break and form as the molecules move

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(5) KBr is added to a beaker containing water. Will it dissolve, and if so, what interactions will
facilitate the dissolution process?

(6) In which of the following diagrams are hydrogen bonds correctly shown (hydrogen bonds are
indicated by a dashed line)?

Functional Groups
- For functional groups that you are expected to recognize, identify, and recall properties
(polar/nonpolar/charged), reference the chart found in the lecture slides

(7) Identify the functional groups in the following molecules.

A) B) C)

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Lecture 1.3
Carbohydrates
- General formula: (CH2O)n , where n ≥ 3
- Can differ from each other in several ways: length of carbon backbone, arrangement of
atoms (aldose vs ketose), orientation of hydroxyl groups
- Different structures will lead to different functions and affect the chemical
properties of the carbohydrates
- In aqueous solution, a ring form of carbohydrates (n ≥ 5) predominates because it is
more stable
- Monomer: monosaccharides (simple sugars such as glucose)
- Monosaccharides are linked together with glycosidic bonds (or linkages), which requires
a dehydration reaction (condensation reaction) that removes one molecule of water to
form the bond
- Based on the orientation of carbon-1 OH groups, an 𝛼-glycosidic bond or
𝜷-glycosidic bond forms
- 𝛼-glycosidic bond points DOWN, 𝜷-glycosidic bond points UP
- Starch is an 𝛼-glucose polymer with energy storage capacity in plants – mixture of
branched and linear polymers
- Glycogen is an 𝛼-glucose polymer with energy storage capacity in animals – highly
branched
- Cellulose is a linear 𝜷-glucose polymer that helps with cell wall structure of plants
- Hydrogen bonding between parallel cellulose polymers
- Chitin is a structural polysaccharide found mainly in fungi cell walls and animal
exoskeletons, and it is comprised of N-acetylglucosamine monomers

(8) What is the difference between an aldose and ketose?

(9) List some differences between starch, glycogen, cellulose, and chitin. Consider each of their
primary functions and structure.

(10) How many water molecules will be consumed in breaking down a 250-residue cellulose
chain?

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Lipids
- Defined by their solubility rather than chemical structure: hydrocarbons that are
insoluble in water
- Do not have a common structure (unlike the other macromolecules)
- Fatty acid is a hydrocarbon chain bonded to a carboxyl (—COOH) functional group
- Saturated: only single bonds between carbon atoms (saturated with as many
hydrogen atoms as possible) → solid at room temp, linear, pack well together
- Unsaturated: one or more double bonds in the hydrocarbon chain → liquid at
room temp, trans vs. cis double bonds
- Naturally occurring unsaturated fats have cis double bonds that create kinks in
the structure (H atoms on same side of double bond)
- Trans fatty acids have trans double bonds that do not create kinks in the
structure (more linear, H atoms on opposite sides of double bond)
- Steroids can be recognized by their bulky, four-fused-ring structure
- Differ from each other based on the functional groups attached to different
carbons in the hydrophobic rings
- Fats form through condensation reactions between a hydroxyl group of glycerol and
carboxyl group of a fatty acid chain
- Triglyceride: 3 fatty acid chains + 1 glycerol head → release 3 water molecules
through the reaction
- Phospholipids are amphipathic – polar head (glycerol, phosphate, charged group) and
nonpolar tails (two fatty acid chains)
- Because of their structure, phospholipids spontaneously form bilayers in aqueous
solutions (this is how the cell membranes are structured – phospholipid bilayers)

(11) Draw the general structure of a phospholipid bilayer and label the hydrophobic and
hydrophilic portions.

(12) Compare and contrast cis vs. trans fatty acids. What is their structure? Which has a higher
melting point? Why?

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Lecture 1.4
Nucleic Acid Structure
- Monomer: nucleotide (3 parts: pentose sugar, nitrogenous base, phosphate group)
- Nucleoside: nucleotide without a phosphate group (so just the 5 carbon sugar
plus a nitrogenous base)
- Basically: nucleoside + phosphate → nucleotide
- Nitrogenous base attaches to the 1’ carbon and phosphate group to the 5’ carbon
- Pyrimidines have a single ring structure while purines have a double-fused ring structure
- Purines: A and G Pyrimidines: C, U, and T
- Mnemonic that might help:
- Purines: PURe As Gold
- Pyrimidines: CUT a PY (pie)
- Nucleotides polymerize by condensation reaction, forming phosphodiester bonds
- Phosphodiester bond forms between the 5’ phosphate group of the NEW
nucleotide to the 3’ hydroxyl group of the already existing chain → ALWAYS ADD
to the 3’ END of the existing chain at the hydroxyl end
- The backbone is directional: grows in the 5’ → 3’ direction (and only in this
direction) → IMPORTANT!

DNA (Deoxyribonucleic Acid)

- Pentose sugar: deoxyribose [H on 2’ carbon]
- Chargaff defined some rules that DNA follows (based on observation):
- % adenine = % thymine [ratio of A to T is nearly always 1:1]
- % guanine = % cytosine [ratio of G to C is nearly always 1:1]
- So basically, A pairs with T and vice versa; C pairs with G and vice versa
- And also….. A + G = T + C OR # purines = # pyrimidines
- Franklin’s X-ray diffraction data suggested that DNA was a double-stranded helix with
phosphates on the outside of the helix
- Watson and Crick build a physical model of DNA based on Chargaff’s rules and Franklin’s
X-ray diffraction experiment
- Across the two strands within the helix, nitrogenous bases form hydrogen bonds with
each other: 2 hydrogen bonds between A—T and 3 hydrogen bonds between C—G
- DNA has two different-sized grooves: major groove and minor groove → important for
protein interactions with DNA
- DNA stores and transmits biological information: sequence of nucleotides carries
information and DNA structure allows it to transmit this information as necessary

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RNA (Ribonucleic Acid)

- Pentose sugar: ribose [OH on 2’ carbon]
- RNA is mostly single stranded
- However….the bases of RNA typically form hydrogen bonds with complementary
bases on the SAME strand (this is its secondary structure)
- A—U and C—G
- This causes the RNA strand to fold over
- RNA can also have tertiary structure when the secondary structures fold into more
complex shapes
- mRNA (messenger RNA): synthesized from DNA and carries genetic information to the
ribosome for protein synthesis
- 2’ —OH (hydroxyl) group on ribose makes RNA much more reactive (and therefore also
much less stable) than DNA

(13) What are the key features of DNA structure? How do these relate to DNA’s function?

(14) What is the complementary DNA strand to the following sequence? Make sure to include
directionality.
5’ TAC GCC ACA TTG CGA AGT AAT ATC 3’

(15) What structural features are different between DNA and RNA?

(16) Rank the following DNA molecules from lowest (1) to highest (5) melting point.
16% guanine, 38% adenine, 42% cytosine, 6% thymine, 24% cytosine

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Lecture 1.5
Central Dogma
- DNA → RNA → Protein is the typical flow of biological information in organisms
- Genes are segments of DNA that carry hereditary information, so gene expression is the
process of translating that information into functioning molecules
- Srb & Horowitz tested the one-gene, one-enzyme hypothesis through a biochemical
pathway that synthesized arginine as its final product
- They placed each mutant strain on a minimal nutrition medium with and with
certain supplements (the supplements were other substances involved in the
pathway)
- They then observed for growth of the organism: if the organism is unable to
convert one compound to another, then it lacks the enzyme required for that
conversion
- Therefore, the mutation is in the gene that codes for that malfunctioning enzyme
- Because genes contain the information for all proteins in an organism, and not just
enzymes, the one-gene, one-enzyme hypothesis was revised to: one-gene,
one-polypeptide [one gene determines one polypeptide]

Protein Production Based on Information in Genes

- mRNA carries information from DNA to site of protein synthesis (ribosomes)
- Transcription: RNA polymerase synthesizes mRNA transcript based on the DNA
sequence (complementary base pairing)
- Translation: mRNA transcript is translated to a protein (amino acid sequence) at
the ribosome (based on the codon chart)
- Genetic code is made up of triplets called codons
- Each codon specifies one singular amino acid, but there are more codons than
there are amino acids (43 = 64 codons, 20 amino acids + STOP codons)
- Genetic code is redundant (more than 1 codon specifies each amino acid) but
NOT ambiguous (no codon specifies more than 1 amino acid)
- Genetic code is also conservative: when several codons specify an amino acid,
the first two bases in the codon are usually identical
- Start codon: AUG (codes for methionine)
- 3 stop codons: UAA, UAG, UGA (these don’t code for any amino acid)
- DNA serves as a template for the mRNA: the 5’ → 3’ strand of DNA is the coding strand
while the 3’ → 5’ strand is the template strand
- The TEMPLATE strand is used for complementary base pairing to yield the mRNA
transcript in transcription
- mRNA transcript is read from 5’ → 3’ to be translated into the polypeptide

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Amino Acids
- Amino acids are the monomers to proteins (there are 20 amino acids)
- Typical structure of an amino acid: carbon with an amino group on one end, carboxyl
group on the other end, and an R side chain
- The R-group makes each amino acid unique and gives it defining characteristics
(will help determine how the amino acid behaves chemically)
- Common R-group characteristics:
- Charged (+1/-1): hydrophilic, attract oppositely charged ions of molecules
- Polar (𝛿+/𝛿-): hydrophilic, form hydrogen bonds with other polar molecules
- Nonpolar: hydrophobic, aggregate in interior of protein (hydrophobic interaction)
- Special cases:
- Glycine: small [R-group is a singular hydrogen atom]
- Proline: rigid [R-group has a ring structure due to covalent bond to amino group]
- Cysteine: can form a disulfide bridge [R-group contains a sulfur atom]
- Proteins form when amino acids polymerize through condensation reactions, forming a
peptide bond between the carboxyl group of one amino acid and the amino group of the
other [so the peptide bond is always between a C atom and a N atom]
- Polypeptide chains have a directionality: side of the chain with the amino group is the
N-terminus and side with the carboxyl group is the C-terminus
- The chain always grows at the C-terminus (new amino acids are always added to
the C-terminus)

(17) Based on the following DNA template strand, determine the mRNA transcript and the
resulting polypeptide chain. Be sure to include directionality in your answer.
3’ TAC GAG CAC TGC TAA ATT 5’

(18) Based on the following DNA coding strand, determine the resulting polypeptide chain. Be
sure to include directionality in your answer.
5’ ATG GAA GCC TAC CAG TGA 3’

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(19) Looking at the structures of the following amino acids, classify each as
polar/nonpolar/charged or one of the special cases.
A) B) C)

D) E) F)

(20) The diagram below depicts a peptide chain. Label the N-terminus, C-terminus and identify
the peptide bonds. Circle the amino acids and try to determine if they are polar, nonpolar, or
charged. If you wanted to add a new amino acid to the chain, where would it go?

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(21) When synthesizing a polypeptide chain, 182 water molecules were produced. How many
amino acids are in the chain?

(22) Summarize the flow of information starting from the DNA molecule to produce a
polypeptide chain. Think about the location of these processes within a cell and the
directionality of the polymers involved. Try drawing it out – this can be confusing and there is a
lot to keep track of, so this is a good exercise to test your understanding of these processes.

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Lecture 1.6
Protein Structure
- Order of amino acids will dictate how a protein folds into its 3D structure
- Primary structure: sequence of amino acids stabilized by peptide bonds
- Secondary structure: repeating patterns in the structure of the polypeptide that are
stabilized by hydrogen bonds to form 𝛼-helices and 𝛽-pleated sheets
- Tertiary structure: 3D structure of polypeptide stabilized by R-group interactions (not
covalent bonds, but weaker interactions between R-groups of amino acids such as
hydrogen bonding, disulfide bonds, hydrophobic interactions)
- Quaternary structure: interactions between multiple polypeptide chains (must have
more than 1 polypeptide to have quaternary structure)

Protein Folding
- A protein’s final folded 3D structure will determine its function
- Primary structure determines the 3D structure which determines biological
activity of the protein (structure determines function!)
- Anfinsen hypothesized that a denatured protein could re-fold into a functional 3D
structure: this is because proteins fold spontaneously (energetically favorable process)
- Hydrophobic amino acids want to fold into the center where they will be
shielded from water
- Similarly, hydrophilic amino acids want to be on the exterior where they can
interact with water
- Protein misfolding can lead to disease: when a polypeptide misfolds, it has a new
structure and therefore an altered function as well (whether it is a loss of function or a
gain of function) – it can have significant impacts biologically
- Environmental conditions can also affect protein structure and function:
- Increases in temperature: proteins tend to denature in higher temperatures
- Changes in pH (H+ concentration): this can impact the chemical interactions,
especially in charged and polar amino acids
- Changes in polarity of substances surrounding a protein: this will impact chemical
interaction
- If a protein with predominantly polar amino acids was placed in a
nonpolar solvent, that would not work out well
- Binding to another protein or molecule will often lead to a conformational change in the
protein

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(23) Mad Cow Disease is a brain illness that occurs in bovine species. This disease is progressive,
and incurable. Sick cows typically show lack of coordination, nervousness, and violence due to
the degradation of their gray matter. It takes 5 to 7 years for the disease to fully progress,
meaning scientists do not know when a cow has Mad Cow disease until after its death. Research
shows that Prions are responsible for the deterioration of gray matter. A Prion is a misfolded
protein that does not interact with the brain like a wild-type protein would. Typically, prions are
misfolded due to the 14th amino acid Alanine in the polypeptide being substituted for Serine.
Explain what stage of protein folding was interrupted and how the final shape of the protein will
be affected.

(24) Hypothetical protein X functions well in aqueous solution. Which of the following amino
acids (based on their structure) are you likely to find on the interior of the protein structure.
Select all that apply.
A) B) C)

D) E)

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