Final Exam Information
BIOL 112 Term 1 2022W
Date: Tuesday, Dec 20th, 2022 at 8:30 am
Room:
Buchanan D – Room 201
Exam Details
1. Individual Exam - 2hrs
Multiple Choice/True/False option Questions (>40) + Open Response Questions
(3 muti-part -no longer than 1 page double sided)
● You are permitted a one-page, 8.5 X 11 inch, double-sided review sheet to use
during the Individual Exam.
● Please bring UBC Identification - all ID’s will be checked during the exam.
Testable Content for the Final
1. Any content not yet tested i.e., on the midterm
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Unit 2-2: PCR (DNA replication in vitro)
Unit 2-3: DNA replication in vivo -inside cells
Unit 3-4: Translation - Electron Micrographs
Unit 3-5: DNA mutations
Unit 3-6: Regulating gene expression: Operons
Unit 4: All of Metabolism.
2. Content from Tutorials and Mastery Learning Modules (MLMs)
All Tutorial/MLM content is testable for the final exam!
● Proteins/Transport
● Transcription/Translation
● DNA mutations
● Operon mutations
● Chemistry for biology
● Transcription - gene structure/upstream/downstream
● PCR
Think about how we can integrate these concepts into what you learned later in
the course!
3. Other Content/Units
● Unit 1: We will NOT directly test you on Unit 1 BUT focus on concepts
that are re-introduced throughout the term e.g., noncovalent interactions,
comparing cells (euk vs bac), transport, proteins, etc
● Units 2.1; 3.1; 3.2; 3.3; 3.4 You should know the general concepts. You
should know how to transcribe and translate a gene!
Copyright: BIOL 112: Biology of the Cell, University of British Columbia
Unit 2-2: DNA replication in vitro – Polymerase chain reaction (PCR)
Targeted:
▪
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).
▪
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 2-3: DNA replication in vivo (inside cells)
Targeted:
▪
Compare and contrast DNA replication in vitro (PCR) and in vivo (in cells).
▪
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.
Copyright: BIOL 112: Biology of the Cell, University of British Columbia
Unit 3-4: Translation
Targeted:
▪
List RNAs involved in the process of translation and describe their roles.
▪
Describe the features of the genetic code (“universal”, “redundant” and “nonoverlapping”).
▪
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, 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
o
o
o
Identify the macromolecules that can be observed in each image.
Label the directionality (polarity) of the macromolecules.
Identify the direction of transcription by RNA polymerase.
Differentiate between electron micrographs of transcription and
translation occurring in bacterial and eukaryotic cells.
Unit 3-5: DNA mutations
Prior Knowledge:
▪ Compare the general chromosomal structure in bacterial cells versus eukaryotic
cells.
▪ Explain the terms genotype and phenotype.
▪ Compare the definitions of genome, chromosome and gene in terms of the DNA in
the cell.
Copyright: BIOL 112: Biology of the Cell, University of British Columbia
Targeted:
▪
Identify the different types of point (base substitution) mutations: 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.
Unit 3-6: Regulating gene expression: the bacterial mal and lac operons as examples
Targeted: General principles in gene regulation and the structure of a bacterial operon
▪
Explain how gene expression may be regulated at the transcriptional and posttranscriptional levels.
▪
Contrast the general mechanisms of positive and negative transcriptional regulation
with respect to transcription factor binding and gene expression.
▪
Describe what is meant by basal level transcription and constitutive transcription.
▪
Identify the structural components of a bacterial operon and define the roles of each
component in operon regulation.
Targeted: Gene regulation in bacteria - operons:
▪
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
promoter.
▪
Describe and compare “strong” vs. “weak” promoters.
▪
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
▪
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.
Unit 4 Learning Objectives
Big picture learning objective for Unit 4:
▪
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
o
o
o
o
o
Glycolysis
Fermentation
Pyruvate processing and the Citric Acid Cycle
Oxidative Phosphorylation
Photophosphorylation
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.
Targeted:
▪
Distinguish between anabolic and catabolic reactions
▪
Describe the types of nutrients required for metabolic function for the cell.
Copyright: BIOL 112: Biology of the Cell, University of British Columbia
▪
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
Targeted:
▪
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
Targeted:
▪
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.
▪
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
Copyright: BIOL 112: Biology of the Cell, University of British Columbia
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.
Targeted:
▪
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
Targeted:
▪
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.
▪
Predict and describe how metabolic inhibitors such as dinitrophenol (DNP) can
alter the function of the ETC.
Copyright: BIOL 112: Biology of the Cell, University of British Columbia
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.