Copyright: BIOL 112: Biology of the Cell, University of British Columbia - Modified Jan 3, 2024

Learning Objectives – Biol 112 Winter Session 2023

By the end of BIOL 112, a successful student should be able to:

1. Describe the general cellular machinery and processes of replication, transcription,
translation, and energy transformation.
2. Apply your knowledge of the chemical properties of biomolecules (proteins, nucleic
acids, lipids, carbohydrates) to explain the structure and function of cellular
structures and organelles.
3. Discuss how the fundamental principles of chemistry and physics dictate cellular
processes, and energy transformations within cells.
4. Using basic thermodynamics, outline how a cell harnesses energy from sugar to
make ATP and energy from light to make reduced carbon compounds.
5. Work in small groups to analyze, discuss, and solve problems in the context of cell
biology and biochemistry.
6. Practice working and communicating in small group settings and actively contribute
to team-based problem solving.
7. Interpret information on figures and draw conclusions based on descriptive or
graphical data in the context of cell biology and biochemistry.
8. Clearly and succinctly communicate (in writing) evidence-based scientific ideas
related to cell biology and biochemistry.
9. Describe the complexity and interrelationship between cellular components and
describe the role of biochemical pathways in cellular function.
10. Apply your knowledge to solve problems similar to questions and problems asked
during class as clicker questions, short answer problems, or worksheet activities.

Continue to the next page for Learning Objectives for each topic.

Note: There are four Units in the course, and each module inside the unit is
numbered, e.g. for Unit 1, there is Unit 1-1, 1-2, below.
 Copyright: BIOL 112: Biology of the Cell, University of British Columbia - Modified Jan 3, 2024

Unit 1 Learning Objectives-Cells and Membranes

Unit 1-1: General properties of cells

Prior knowledge:

▪ Discuss diversity in cell size, structures; cells as organisms versus cells in

organisms; unicellular versus multicellular.
Targeted:

▪ Summarize the critical components of cell theory.

▪ List and evaluate the characteristics that define cells as the smallest unit of life.

▪ Compare and contrast the structural properties of bacterial and eukaryotic cells

▪ Compare general chromosomal structure and location of the genomes in bacterial

cells versus eukaryotic cells.

▪ Explain the endosymbiotic theory in the evolution of eukaryotic cells.

Unit 1-2: Bacterial and Eukaryotic Cell Growth in the Lab

Targeted:

▪ Describe what is meant by growth in a prokaryotic organism, distinguishing between

growth and division of individual cells, and growth of a population of cells.

▪ Identify the four phases of population growth in a batch culture and in the
associated growth curve graph - lag phase, exponential (log) phase, stationary
phase, and death phase.

▪ Compare and Contrast a population of cells in lag phase, exponential phase,

stationary phase, and death phase in terms of division rate and cell survival.
 Copyright: BIOL 112: Biology of the Cell, University of British Columbia - Modified Jan 3, 2024

Unit 1-3 Chemistry for Biology

Prior knowledge:

▪ Identify how the highly electronegative atoms (for example O and N) lead to uneven
electron sharing and permanent dipoles when bonded to other biologically relevant
atoms.

▪ Identify whether a molecule or group on a molecule is polar/nonpolar,

neutral/charged, hydrophobic/hydrophilic/amphipathic.
Targeted:

▪ Predict the types of non-covalent interactions that can form between functional
groups within a molecule or between molecules.

Unit 1-4: Introduction to macromolecules in cells

Prior knowledge:

▪ List the four major categories of macromolecules in cells.

Targeted:

▪ Give an example of a cellular structure or organelle where each type of

macromolecule can be found in prokaryotic or eukaryotic cells.

▪ Describe and explain the concepts of asymmetrical monomer polarity and

macromolecule directionality, and why these concepts don’t apply to lipids.

▪ For each of the polymeric macromolecules (nucleic acids, proteins, carbohydrates)

list and identify the monomers, types of covalent bonds linking the monomers
together, the directionality of the macromolecules, and the reason for the
directionality.

▪ Explain and relate the chemical properties of functional groups to

macromolecule polymerization, directionality, and non-covalent interactions.

▪ Recognize the general structure, chemical properties and functional groups of

monomers that make up each type of macromolecule.

▪ Refer to Chemistry for Biology Learning objectives, which will be featured throughout
the course.
 Copyright: BIOL 112: Biology of the Cell, University of British Columbia - Modified Jan 3, 2024

Unit 1-5: Fluid Mosaic Model of Membranes – Phospholipids, self-assembly of

bilayers, membrane proteins

Targeted:

▪ Predict which structures (micelles or bilayers) will form when different kinds of lipids
are mixed with water .

▪ Explain the amphipathic nature of phospholipids, and which non-covalent

interactions will likely form when phospholipids are mixed with water.

▪ Explain how thermochemistry and thermodynamic system stability, especially in

terms of the entropy of water, leads to the spontaneous assembly of phospholipid
bilayers (i.e. the hydrophobic effect).

▪ Identify how proteins are embedded in membrane bilayers in terms of hydrophilic

and hydrophobic groups.

▪ Describe how the cell membrane is both a container and a barrier using the Fluid
Mosaic model of biological membranes.

Unit 1-6: Membrane Transport

Prior knowledge:

▪ Distinguish between the processes of diffusion and osmosis.

Targeted:

▪ Predict the permeability of various types of molecules across lipid bilayers based
on size and charge.

▪ Distinguish between the different types of membrane transport (simple diffusion,

facilitated diffusion and active transport) in terms of concentration dependence,
protein transporters, and energy requirements.

▪ Compare and contrast membrane transport proteins (carriers versus channels).

▪ Plot a transport graph comparing the concentration ratios of molecules across

membranes over time and predict the type of transport occurring.

▪ Predict the type of transport occurring based on the transport graph data.
 Copyright: BIOL 112: Biology of the Cell, University of British Columbia - Modified Jan 3, 2024

Unit 1-7: Proteins – Structure and self-assembly

Targeted:

▪ Describe and recognize the structural components of proteins, including the

monomers, the N- and C- terminal directionality, and the reason for this
directionality.

▪ Draw the generic structure of an amino acid and identify the key functional groups.

▪ Identify a peptide bond between amino acyl residues in a polypeptide (i.e. be able
to circle it on a structure).

▪ Classify amino acids based on the hydrophilic/hydrophobic properties of their side

chains (R-groups).

▪ Distinguish between primary, secondary, tertiary, and quaternary structure of

polypeptides and the molecular interactions that give rise to them.

▪ Predict the likely R-group properties of amino acids based on their location within a
protein’s folded structure (i.e. interior vs. exterior)

▪ Define protein denaturation and predict the effects of protein denaturation on

structure and function.

▪ Predict the effects of changing amino acids on protein structure and function.

▪ Describe the spontaneous assembly and folding of proteins using the relative
terms; stability, bond strength, spontaneous and entropy (i.e. the hydrophobic
effect).

▪ Describe allosteric changes in protein structure as a control mechanism to alter

enzyme/protein activity.
 Copyright: BIOL 112: Biology of the Cell, University of British Columbia - Modified Jan 3, 2024

Unit 2 Learning Objectives-transcription and translation

Unit 2-1: Nucleic Acids – Structure, DNA assembly and organization

Targeted:

▪ Explain the functions of DNA in cells and between generations of cells.

▪ Describe and recognize the structural components of nucleic acids, including the
monomers, the directionality, and the reason for the directionality.

▪ Describe the key features of the DNA double helix, such as the sugars,
phosphodiester bonds, bases; base pairs; base pair geometry; the major/minor
grooves.

▪ Identify the non-covalent interactions that determine DNA structure, such as base
stacking and H-bonds.

▪ Explain how the entropy of water drives the hydrophobic effect with respect to DNA.

▪ Identify key structural differences between DNA and RNA.

▪ Label a schematic diagram of double stranded DNA to show the 3’ and 5’ ends,
including the functional group found at each 3’ and 5’ position.

▪ Know and apply the Chargaff’s base pair rules.

Unit 2-2: Biological information flow

Targeted:

▪ Describe the biological information flow from DNA to proteins in cells, and the role
of transcription and translation in this process.

▪ Distinguish between the processes of replication, transcription, and translation.

▪ Describe the role of messenger RNA molecules as a link between genes and
proteins.
 Copyright: BIOL 112: Biology of the Cell, University of British Columbia - Modified Jan 3, 2024

Unit 2-3 Transcription – Gene structure

Targeted:

▪ Draw the structure of transcription units (a gene) in both bacteria and eukaryotes,
clearly differentiating between regulatory and transcribed regions.

▪ Identify a promoter region on a transcription unit (gene).

▪ Explain and Identify upstream and downstream regions of the genome when used
to describe relative location of gene structures.

▪ Explain the difference between the template strand and the non-template (coding)
strand in DNA.

▪ Compare and contrast the structure of the transcription units in bacteria and
eukaryotes.

Unit 2-4: Transcription –DNA to RNA

Targeted:

▪ Explain how the interaction of a transcription factor and the promoter of a gene
leads to repression or the initiation of transcription.

▪ Describe the role of RNA polymerase in transcription, and role of DNA-binding

proteins in the initiation of transcription.

▪ Predict the RNA sequence transcribed from the DNA sequence of a transcription
unit.

▪ Predict the types of non-covalent interactions likely to form between DNA and a
protein involved in transcription.

▪ Compare and contrast how proteins involved in transcription in bacteria and

eukaryotes recognize a promoter.
 Copyright: BIOL 112: Biology of the Cell, University of British Columbia - Modified Jan 3, 2024

▪ List the various eukaryotic mRNA processing events – 5’-capping, splicing, and
poly-adenylation (polyA tails).

▪ Explain how RNA splicing can be used to produce different mature mRNA
transcripts/proteins from the same pre-mRNA and determine the correct splicing
pattern for any mature mRNA.

▪ Compare and contrast the structures and functions of the different types of RNA
molecules: rRNA, tRNA, mRNA.
Unit 2-5: Translation-RNA to protein

Targeted:

▪ List RNAs involved in the process of translation and describe their roles.

▪ Describe the features of the genetic code (“universal”, “redundant” and

“non-overlapping”).

▪ Explain the function of aminoacyl tRNA synthetase enzymes and why they are
described as “the translators” of the genetic information.

▪ Describe the roles of the ribosome binding sites (RBS) in bacteria and eukaryotes,
the start codon, and stop codons on a mRNA.

▪ Explain what is meant by “wobble” in tRNA binding.

▪ Describe the general events in the three-step process of translation (initiation,

elongation, and termination) and the directionality of translation.

▪ Predict the anticodon of a tRNA for a given amino acid using the codon table.

▪ Translate a stretch of DNA coding sequence into its polypeptide product.

▪ Interpret electron micrographs of isolated DNA/RNA/ribosome complexes during

transcription and translation in bacterial and eukaryotic cells:

o Identify the macromolecules that can be observed in each image.

o Label the directionality (polarity) of the macromolecules.
 Copyright: BIOL 112: Biology of the Cell, University of British Columbia - Modified Jan 3, 2024

o Identify the direction of transcription by RNA polymerase.

o Differentiate between electron micrographs of transcription and
translation occurring in bacterial and eukaryotic cells.

Unit 2-6: DNA mutations and genome editing

Prior Knowledge:
▪ Explain the terms genotype and phenotype.

▪ Compare the definitions of genome, chromosome and gene in terms of the DNA in
the cell.

Targeted:

▪ Identify the three different types of point mutations (when one base in the DNA is
changed): missense, nonsense, and silent mutations.

▪ Predict the effects (consequences) of point (base substitution) and deletion

mutations in different locations of transcription units on the genotype and phenotype
of a cell.

▪ Predict the effects of mutations in coding vs noncoding regions of the genome.

▪ Predict the effects of a point mutation in the coding region of the gene on the
resulting amino acid sequence and analyze how/if this will change the protein
structure/function.

▪ Describe the role of clustered regularly interspaced short palindromic repeats

(CRISPR), and the nuclease Cas9, in bacterial defence against viruses.

▪ Explain the roles of guide RNA, Cas9, and target DNA in CRISPR/Cas9 genome
editing.
Unit 2-7: Regulation of Gene Expression

Targeted: General principles in gene regulation

▪ Explain how the presence of a nutrient results in the induction of the operon
encoding the genes to digest that nutrient.
 Copyright: BIOL 112: Biology of the Cell, University of British Columbia - Modified Jan 3, 2024

▪ Explain how gene expression may be regulated at the transcriptional and

post-transcriptional levels.
▪ Contrast the general mechanisms of positive and negative transcriptional regulation
with respect to transcription factor binding and gene expression.
▪ Explain why differential gene expression of the genome is required to develop
specialized cells types in multicellular organisms, or to respond to changes in the
environment.

▪ Describe what is meant by basal level transcription and constitutive transcription.

Targeted: Gene regulation in bacteria - operons:

▪ Identify the structural components of a bacterial operon and define the roles of each
component in operon regulation.

▪ Explain the logic of the function and regulation of an operon relative to the
availability of a food source (for example, lactose or maltose).

▪ Draw a correct representation of an operon that includes the structural genes in the
operon, the promoter and operator regions, as well as the regulatory gene with its
product and promoter.

▪ Describe and compare “strong” vs. “weak” promoters.

▪ Predict the binding of positive or negative regulator proteins to the operator region
of an operon based on the presence and absence of the signal molecule.

▪ Explain how the presence of a signal molecule results in the induction of an operon
that is positively regulated.

▪ Predict what happens to transcription, if there are mutations in the DNA sequences
of either the gene encoding the regulator protein or the operon elements (operator,
promoter, genes, etc.).

▪ Apply the principles of gene expression learned from lac or mal operon to explain
other examples of transcriptional regulation.
 Copyright: BIOL 112: Biology of the Cell, University of British Columbia - Modified Jan 3, 2024

Unit 3 Learning Objectives-DNA replication and amplification

Unit 3-1: DNA replication in vivo (inside cells)

▪ Compare and contrast DNA replication in vitro (PCR) and in vivo (in cells).

▪ Place DNA replication within the growth phases for bacterial or eukaryotic cells (i.e.
lag, log/exponential, stationery and death phase).

▪ Explain the logistics of the DNA replication process including how the cell solves the
problems of:
o Separating the DNA strand.

o Replicating both strands simultaneously in the 5’ to 3’ direction.

o Synthesizing primers and providing primers for the leading and the lagging
strands during replication (DNA synthesis).
o Distinguish between and label the leading and the lagging strands of DNA in
a replication fork.

▪ Explain what an Okazaki fragment is and its role in replication.

▪ Predict the types of non-covalent interactions that enable interactions between DNA
and DNA-binding proteins.
Unit 3-2: DNA replication in vitro – Polymerase chain reaction (PCR)

▪ Explain why PCR is such an important technique in molecular biology (i.e. why do
we care about making lots of copies of a specific piece of DNA) and identify practical
uses of PCR.

▪ Describe the three key steps in polymerase chain reactions; denaturation, annealing
and extension, and explain what role these play in the replication of DNA in a test
tube.

▪ List the components needed (in a test tube) to start a PCR amplification experiment.

▪ Describe the role of the four deoxyribonucleoside triphosphates (dNTPs) used in

DNA synthesis (dATP, dGTP, dCTP, dTTP).
 Copyright: BIOL 112: Biology of the Cell, University of British Columbia - Modified Jan 3, 2024

▪ Identify the structural “end” of a DNA molecule where dNTPs are added during DNA
synthesis.

▪ Construct a representation of template DNA, primers, and their orientation to each

other using the directionality of DNA.

▪ Predict what primers would be needed to amplify a given piece of double stranded
DNA.

▪ Predict the products of an amplification reaction given locations of primers on a

DNA.

Unit 4- Metabolism
Big picture learning objective for Unit 4:

▪ Recognize the ubiquity of central metabolic pathways across the tree of life.

▪ Compare (remembering the first law of thermodynamics) and contrast (using the
vocabulary of oxidation and reduction) the functions of mitochondria and
chloroplasts.

▪ Identify the functional inputs and outputs for each of the metabolic processes (and
any combination of these) and how they contribute to cellular metabolism:
o Glycolysis
o Fermentation
o Pyruvate processing and the Citric Acid Cycle
o Oxidative Phosphorylation
o Photophosphorylation
o The Calvin Cycle

Unit 4-1: Metabolism overview – Energy and chemical reactions

Prior Knowledge:

▪ Explain the role of the enthalpic (ΔH) and entropic (ΔS) factors in the Gibbs Free
Energy (ΔG) equation.
 Copyright: BIOL 112: Biology of the Cell, University of British Columbia - Modified Jan 3, 2024

Targeted:

▪ Distinguish between anabolic and catabolic reactions

▪ Describe the types of nutrients required for metabolic function for the cell.

▪ Explain how the high energy phosphate bonds of ATP make it a good energy
carrier, for example, in anabolic polymerization reactions of a nucleic acid strand.

Unit 4-2: Cellular respiration overview and redox reactions

▪ In eukaryotes and bacteria, locate the structures and compartments (i.e.

mitochondria and chloroplast) in which the various components of the complete
pathway of cellular respiration occur.

▪ Define and identify redox reactions using examples of organic compounds and high
energy electron carriers.

▪ Identify reduced and oxidized states of organic molecules and high energy electron
carriers.
Unit 4-3: Glycolysis and Fermentation

▪ Locate glycolysis in bacterial and eukaryotic cells.

▪ Identify the inputs and the outputs of the glycolytic pathway.

▪ Describe the process of substrate level phosphorylation in generating ATP in

glycolysis and identify where this type of ATP synthesis occurs.

▪ Describe the function of NADH produced and predict the fate of the NADH that is
produced during glycolysis.

▪ Discuss the role of fermentation and how end products such as lactate and ethanol
play a role in NAD+ regeneration.

▪ Identify the electron acceptors in fermentation compared to chemiosmosis.

 Copyright: BIOL 112: Biology of the Cell, University of British Columbia - Modified Jan 3, 2024

▪ Evaluate the redox state of C atoms in glucose, fermentation end products such as
lactate, and CO2 and use this to explain the relative amounts of ATP generated by
fermentation and respiration.

▪ Compare the efficiency of ATP synthesis by cellular respiration to that of

fermentation
Unit 4-4: Acetyl-coA synthesis and the citric acid cycle

Note: the citric acid cycle is also called the Krebs or tricarboxylic acid (TCA) cycle.

▪ Contrast the cellular locations of acetyl-coA synthesis and the citric acid cycle in
bacterial and eukaryotic cells.

▪ Recognize examples of oxidation-reduction reactions in acetyl-coA synthesis and

the citric acid cycle.

▪ Identify the inputs and the outputs of acetyl-coA synthesis and the citric acid cycle.

▪ Identify when ATP synthesis by substrate level phosphorylation (SLP) occurs during
cellular respiration (this will include glycolysis) or citric acid cycle.

▪ Describe the role of the electron carriers such as NADH and FADH2 in metabolism.

Unit 4-5: Electron transport chain (ETC) and oxidative phosphorylation

▪ Contrast the cellular locations of the ETC/oxidative phosphorylation in bacterial and

eukaryotic cells.

▪ Describe the general process of electron transport and how it creates the proton
gradient in the ETC.

▪ Explain the chemiosmotic theory and how the ETC drives ATP synthesis using a
proton gradient.

▪ Contrast ATP synthesis by substrate level phosphorylation and by oxidative

phosphorylation.
 Copyright: BIOL 112: Biology of the Cell, University of British Columbia - Modified Jan 3, 2024

▪ Predict and describe how metabolic inhibitors such as dinitrophenol (DNP) can
alter the function of the ETC.
Unit 4-6: Photosynthesis – Photophosphorylation and the Calvin Cycle

Targeted:

▪ Identify the locations of photophosphorylation and the Calvin cycle in chloroplasts.

▪ Explain the source of electrons and role of light in generating the proton gradient in
chloroplasts and other oxygenic phototrophs (cyanobacteria).

▪ Trace the path of electrons in oxygenic photosynthetic photosystems starting with

water entering PSII to NADPH.

▪ Compare and contrast photophosphorylation and oxidative phosphorylation with

respect to the locations of the proton gradients and the role/orientation of ATP
synthase.