Midterm Overview (65 mins)

● Parts
○ Individual exam (50 mins) (90% of midterm)
■ MC, multiple answer, Open response (short answers, fill in blanks)
■ CAN HAVE REVIEW SHEET (double sided 8.5 x 11inch)
○ Group exam (15 mins) (10% of midterm)
■ MC only
■ NO REVIEW SHEET
■ Groups of 4
● Content
○ Unit 1: Macromolecules
■ Cells and genomes
■ Introduction to macromolecules
■ Lipids and hydrophobic effect
■ Self assembly of the phospholipid bilayer; Membrane permeability
■ Membrane transport
■ Protein interactions
■ Levels of protein folding
○ Unit 2: Transcription and Translation
■ Nucleic acids and DNA structure
■ Biological information flow
■ Gene structure and transcription
■ Transcription in prokaryotes and eukaryotes
■ Translation
● Practice
○ Weekly Quizzes
■ Introduction
■ Week 1
■ Week 2
■ Week 3
■ Week 4
■ Week 5
■ Week 6
■ Week 7
○ Tutorial
■ MLM Chem for Bio (unit 1)
■ Tutorial #1: Cell Growth (week 3)
■ Tutorial #2: Proteins & Transport (week 4)
■ MLM 2 Transcription & Gene Structure (unit 2)
■ Tutorial 3: Translation (Week 7)
○ Practice problems
■ Unit 1:
● Cell size and Diversity Worksheet
● Unit 1 Practice questions
 ■ Unit 2
● Practice Transcription and Translation Worksheet
● Unit 2 Practice questions

Learning Objectives
1.1 General properties of cells
● Discuss diversity in cell size, structures; cells as organisms versus cells in organisms; unicellular
versus multicellular.
● 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.

1.2: Bacterial and Eukaryotic Cell Growth in the Lab (week 3 tutorial)
● 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.

1.3 Chemistry for Biology (MLM 1)

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

1.4 Introduction To macromolecules in cells

● List the four major categories of macromolecules in cells.
● 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.

1.5 Fluid Mosaic Model of Membranes - Phospholipids, self assembly of bilayers, membrane proteins
● 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.

1.6 Membrane Transport

● Distinguish between the processes of diffusion and osmosis.
● 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.

1.7 Proteins, Structure and self assembly

● 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.

2.1 Nucleic Acids - Structure, DNA assembly and organization

● 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.

2.2 Biological information flow

● 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.

2.3 Transcription - Gene Structure

● 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.

2.4 Transcription - Gene Structure

● 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.
● 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.

2.5 Translation - RNA to protein

● 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.