MBI200 revision questions

Contents
TOPIC 1 - MACROMOLECULES & CELL STRUCTURE ................................................................................ 3
1A. MACROMOLECULES ...................................................................................................................... 3
1B. PROKARYOTIC & EUKARYOTIC CELLS ............................................................................................ 5
1C. CYTOSKELETON ............................................................................................................................. 6
1D. MEMBRANE STRUCTURE .............................................................................................................. 7
TOPIC 2 - DNA REPLICATION, TRANSCRIPTION & TRANSLATION ........................................................... 9
2A. DNA STRUCTURE & REPLICATION ................................................................................................. 9
2B. DNA MUTATION & REPAIR.......................................................................................................... 10
2C. TRANSCRIPTION .......................................................................................................................... 11
2D. TRANSLATION ............................................................................................................................. 12
TOPIC 3 – PROTEIN STRUCTURE & FUNCTION ...................................................................................... 14
TOPIC 3A. PROTEIN STRUCTURE ....................................................................................................... 14
3B. PROTEIN FUNCTION .................................................................................................................... 15
TOPIC 4 – RECOMBINANT DNA TECHNIQUES ....................................................................................... 16
TOPIC 4A. INTRODUCTION TO CLONING .......................................................................................... 16
TOPIC 4B. HYBRIDISATION TECHNIQUES .......................................................................................... 17
TOPIC 4C. COPYING DNA AND RNA IN VITRO ................................................................................... 18
TOPIC 5 – REGULATION OF GENE EXPRESSION .................................................................................... 19
TOPIC 5A. REGULATION OF GENE ACTIVITY IN PROKARYOTES ........................................................ 19
TOPIC 5B. THE LACTOSE OPERON ..................................................................................................... 20
TOPIC 5C. POSITIVE REGULATION OF THE LACTOSE OPERON .......................................................... 21
TOPIC 5D. INTRODUCTION TO REGULATION OF EUKARYOTIC GENE EXPRESSION .......................... 22
TOPIC 5E. REGULATION OF GENE EXPRESSION IN EUKAROTES........................................................ 23
TOPIC 6 – THE CELL CYCLE & APOPTOSIS .............................................................................................. 25
TOPIC 6A. CELL CYCLE & APOPTOSIS................................................................................................. 25
TOPIC 6B. CELL CYCLE CONTROL ....................................................................................................... 26
TOPIC 6C. MOTILITY AND CELL DIVISION .......................................................................................... 27
TOPIC 7 – INTRACELLULAR SIGNALLING AND TRANSPORT................................................................... 29
TOPIC 7A. BIOCHEMICAL MESSENGERS ............................................................................................ 29
TOPIC 7B. CELL PROTEIN TRAFFICKING AND SECRETION ................................................................. 30
TOPIC 8 – MEMBRANE TRANSPORT & ACTION POTENTIALS ................................................................ 32
TOPIC 8A. MEMBRANE TRANSPORT ................................................................................................. 32
TOPIC 8B. MEMBRANE TRANSPORT – PUMPS & CARRIERS ............................................................. 33
TOPIC 8C. SENSITIVE & SELF-SENSITIVE CELLS .................................................................................. 34
TOPIC 9 – APPLICATIONS OF MOLECULAR BIOLOGY ............................................................................ 35
TOPIC 9A. MOLECULAR CELL BIOLOGY & DISEASE ........................................................................... 35
TOPIC 9B. MICROBIAL BIOTECHNOLOGY .......................................................................................... 36
TOPIC 9C. GENETIC ENGINEERING OF PLANTS ................................................................................. 36
TOPIC 1 - MACROMOLECULES & CELL STRUCTURE

1A. MACROMOLECULES
List the four major macromolecules found in cells and the building blocks of each.

What are the relationships between atoms, molecules and macromolecules?

Describe a covalent bond and the non-covalent interactions that bring molecules together.

Describe a condensation reaction and how it is involved in the formation of polysaccharides.

List the two main functions that polysaccharides play in a cell and give an example of a
polysaccharide carrying out each function.

Describe the difference between saturated and unsaturated fatty acids.

List some roles of fatty acids in cells.

Describe the structure of a phospholipid and how this structure contributes to the formation
and function of membranes.
Describe the three components of a nucleotide.

List the purines, pyrimidines, and sugars that make RNA and DNA.

What is the structural difference between a nucleoside and a nucleotide?

What are phosphodiester bonds and how do they form?

Revise concept: in the DNA double helix, the two strands are in an anti-parallel
configuration, with hydrogen bonds holding the strands together and phosphodiester bonds
forming the sugar-phosphate backbone.

List the base-pairing rules and how many hydrogen bonds hold the base pairs together.

List other cellular functions of nucleotides.

Describe the general structure of an amino acid.

Describe the formation of a peptide bond.

Revise concept: the same 20 amino acids make up the proteins of prokaryotes and
eukaryotes.

1B. PROKARYOTIC & EUKARYOTIC CELLS

List some characteristics shared by all cells.

How do prokaryotic and eukaryotic cells differ?

How are eubacteria and archea are differentiated from one another.

Describe the structure and contents of a typical prokaryote.

List and briefly describe the structure and function of the membrane-bound organelles and
other structures that may be found in a eukaryotic cell.

Describe the structure of membranes.

What is the difference between ribosomes found in prokaryotes and eukaryotes?

Briefly describe the basic stages in energy production in an animal cell and the specific
location of each stage (glycolysis, Citric acid cycle, oxidative phosphorylation).

Briefly describe the basic stages of photosynthesis that take place in chloroplasts and the
specific location of each stage (light-dependent reactions, light-independent reactions).

What is the function of the endomembrane system?

Describe the structures and organelles making up the endomembrane system.

1C. CYTOSKELETON
Describe the difference between microtubules, actin filaments and intermediate filaments,
and list the functions of each.

Eukaryotic cells are dynamic. Give one or more examples of a movement they need to
perform.

Describe the assembly and disassembly of actin filaments.

List the roles actin filaments play in a eukaryotic cell.

Give two examples of proteins that interact with actin filaments.

Describe the assembly and disassembly of microtubules.

List the roles microtubules play in a eukaryotic cell.

Give two examples of proteins that interact with microtubules.

List the roles intermediate filaments play in a eukaryotic cell.

List three examples of proteins that form intermediate filaments.

1D. MEMBRANE STRUCTURE

Describe the major functions of membranes in cells.

Describe membrane bilayers and their components, including phospholipids,

transmembrane proteins, glycoproteins, glycolipids.

Describe membrane fluidity, how and why it differs among cellular membranes, and its
importance in cell function.
Revise concept: Alpha helices and beta barrels are regions of proteins that can span a
membrane due to specific patterns of hydrophobic and hydrophilic amino acid side chains. A
hydropathy plot is a graph that shows how hydrophilic or hydrophobic the amino acid
residues in a protein are. Potential transmembrane alpha helices and/or beta barrels can be
predicted based on the pattern of hydrophobic amino acid residues.

List four examples of membrane proteins and their functions.

TOPIC 2 - DNA REPLICATION, TRANSCRIPTION & TRANSLATION

2A. DNA STRUCTURE & REPLICATION

Describe the structure of DNA in detail.

Revise concept: Terminology and components of bases, nucleotides, and nucleosides.

Define the following terms: antiparallel, complementary base pairing, coding strand, right-
handed helix, major groove.

Define the following terms describing DNA replication: semiconservative, origin, bidirectional,
replication fork, Okazaki fragment.

Briefly describe the mechanism of leading and lagging strand replication and the role of the
RNA primer.
Name the proteins at the DNA replication fork and list their functions.

Name the DNA polymerase that carries out most of the DNA replication in prokaryotes.

Name the DNA polymerases involved in nuclear DNA replication in eukaryotes.

2B. DNA MUTATION & REPAIR

What is DNA mutation and what are the general consequences of mutation?

Describe the processes that result in the mutation of DNA.

Describe the consequences of depurination, deamination, thymine dimer formation and

double-stranded breaks on DNA replication.

Explain how transposable DNA elements and infectious agents introduce mutations into
DNA.
Explain the two mechanisms of DNA repair: mismatch repair system and homologous
recombination.

2C. TRANSCRIPTION
What parts of a genome are transcribed?

Describe the directionality and requirements of RNA polymerase, the strand of DNA it
copies, and the overall reaction it catalyses.

Describe the structure of RNA and how it differs from DNA.

List some differences and similarities between RNA polymerases and DNA polymerases.

Describe the components of the core and holoenzyme forms of E. coli RNA polymerase.

Describe prokaryotic transcription initiation and termination signals.

Describe monocistronic and polycistronic mRNAs.

List the major classes of RNA molecules.

Describe differences in prokaryotic and eukaryotic mRNA synthesis.

Describe the structure and function of tRNA and the function of aminoacyl-tRNA
synthetases.

What are the differences between prokaryotic and eukaryotic ribosomes?

List the four binding sites within ribosomes that bind to RNA and what types of RNA bind to
them.

Describe the following structures: polyribosomes, mRNA cap, poly-A tail, codon, anticodon.

2D. TRANSLATION
Describe the “universal” genetic code.

List one example of an exception to the “universal” genetic code.

Explain why the genetic code is described as redundant at the level of the mRNA.
Explain the redundancy in the recognition of the genetic code by tRNAs using the wobble
hypothesis.

How many potential translational frames are there in any mRNA and how many are used?

Describe the three tRNA sites on a ribosome, and what happens at each site.

Describe the initiation, elongation and termination stages of translation.

Give two examples of how some antibiotics inhibit translation.

TOPIC 3 – PROTEIN STRUCTURE & FUNCTION

TOPIC 3A. PROTEIN STRUCTURE

What is the general formula of an amino acid?

Decribe the major groupings of amino acids based on their side chains.

Describe the formation of a peptide bond.

Evolutionarily conserved proteins typically show amino acid sequence homology. Why would
this be?

List the types of noncovalent and covalent interactions that may play a role in determining
the conformation of a polypeptide.

Describe an alpha-helix and a beta-sheet.

Define a polypeptide domain.

Define the 1° (primary), 2° (secondary), 3° (tertiary) and 4° (quaternary) structure of a
protein.

3B. PROTEIN FUNCTION

Define the term ‘ligand’ and give three examples of real proteins binding ligands.

Give an example of a fibrous protein.

Give an example of a globular protein.

List five different ways that enzymes are regulated.

How do motor proteins generate movement?

TOPIC 4 – RECOMBINANT DNA TECHNIQUES

TOPIC 4A. INTRODUCTION TO CLONING

Define the term recombinant DNA molecule.

What do restriction enzymes bind to and what is the end product of the reaction they
catalyse?

Explain how two fragments of restriction enzyme-digested DNA can form a new recombinant
DNA molecule. Include annealing and DNA ligase in your answer.

What is a plasmid vector? List three properties of plasmid vectors that make them useful for
molecular cloning.

Describe the steps in inserting a DNA fragment into a plasmid and amplifying it in bacteria.

Describe the process and purpose of agarose gel electrophoresis.

List two features of an expression vector that make it useful for the large scale production of
proteins.
TOPIC 4B. HYBRIDISATION TECHNIQUES
Describe the conditions under which double-stranded nucleic acid molecules are denatured
and renatured.

What is hybridisation and what types of nucleic acids can hybridise?

What is the difference between a heterologous and a homologous probe?

Describe the process of random priming.

Briefly summarise the technique of Southern blotting.

What does FISH stand for? What might this technique be used for?

How is Northern blotting different from Southern blotting in terms of its process and
purpose?

Explain how in situ hybridisation can be used to reveal gene expression patterns.
TOPIC 4C. COPYING DNA AND RNA IN VITRO
List the main components of a PCR.

Name and describe the 3 steps of a PCR cycle.

Draw a diagram illustrating the binding of a PCR primer pair to a complementary double-
stranded template and extension of the primers by Taq polymerase.

What reaction does reverse transcriptase catalyse? Does it require a primer?

What is the difference between PCR and RT-PCR in terms of process and purpose?
TOPIC 5 – REGULATION OF GENE EXPRESSION

TOPIC 5A. REGULATION OF GENE ACTIVITY IN PROKARYOTES

List four differences between gene regulation in prokaryotes and eukaryotes.

What is the reason for and effect of gene regulation in prokaryotes?

List four ways that a cell can control the proteins it makes.

Describe the basic principles of coordinate regulation, catabolic versus anabolic pathways,
and positive versus negative regulation.

Describe the tryptophan operon of E. coli and its negative regulation using diagrams.
Define the terms operon, promoter, operator, repressor and polycistronic mRNA.

TOPIC 5B. THE LACTOSE OPERON

Draw a basic graph to illustrate usage of glucose and lactose in E. coli.

List the enzymes encoded by the lactose operon and their functions.

Describe the lactose operon and its negative regulation using diagrams.
Explain the terms inducer, inducible, on-off regulation and diauxic growth.

TOPIC 5C. POSITIVE REGULATION OF THE LACTOSE OPERON

List three components important in the positive regulation of the lac operon.

Describe the positive regulation of the lac operon using diagrams.

List three DNA-binding proteins that function in the regulation of gene expression in
prokaryotes.

Revise concept: Understand how some proteins bind to specific regions of DNA, causing
conformational changes that have an effect on gene expression.
TOPIC 5D. INTRODUCTION TO REGULATION OF EUKARYOTIC GENE
EXPRESSION
Are genes gained or lost during development? (Yes/No) Explain your answer.

What is differentiation?

How does differentiation occur?

During development, which usually happens first: differentiation, or rapid cell proliferation?

What are transcription factors?

List the two major types of transcription factors.

Briefly describe two ways that transcription factors influence gene expression in eukaryotic
cells.

Describe the structure of eukaryotic chromosomes. Use the following words in your answer:
chromatin, histone, nucleosome, octamer, supercoiled.
Why do histone tails interact with DNA?

Briefly describe three ways that changing chromosome structure can influence gene
expression.

TOPIC 5E. REGULATION OF GENE EXPRESSION IN EUKAROTES

What is the difference between a cis-regulatory element and trans-regulatory element? Give
some examples of each.

List the different levels of regulation of gene expression in eukaryotes.

Which level of regulation is the most important point of control?

Briefly describe the process of eukaryotic transcription initiation.

Briefly describe three changes that a primary transcript undergoes before it becomes a
mature mRNA.

What is the spliceosome made of?

What is alternative splicing?

Which parts of the mRNA are important in regulating translation initiation?

What is normally the first stage of mRNA degradation?

TOPIC 6 – THE CELL CYCLE & APOPTOSIS

TOPIC 6A. CELL CYCLE & APOPTOSIS

Explain why both the cell cycle and apoptosis are necessary for a multicellular organism.

Briefly describe the events that occur in the following stages of the cell cycle:

G1

G2

Prophase

Metaphase

Anaphase

Telophase

Cytokinesis

Briefly describe the stages of meiosis and how chromosome number changes throughout
the process.

Meiosis I

Meiosis II
How is meiosis different from mitosis?

Briefly describe the events of apoptosis.

What is a caspase and what is the difference between initiator and executioner caspases?

TOPIC 6B. CELL CYCLE CONTROL

List the two main protein families that regulate progression through the cell cycle.

What happens to cyclin levels throughout the cell cycle?

How does cyclin binding affect Cdk activity?

Name the three checkpoints in the cell cycle and briefly describe the purpose of each.
How does p53 control the G1/S checkpoint?

TOPIC 6C. MOTILITY AND CELL DIVISION

Which cytoskeletal proteins are involved in the formation of the mitotic spindle?

Which cytoskeletal proteins are involved in the formation of the contractile ring?

Which cytoskeletal proteins make up part of the nuclear envelope? What changes happen to
these proteins when the nuclear envelope breaks down and reforms?

When are the centrosomes duplicated?

What is the role of the kinetochores?

Describe the role of motor proteins in mitosis.

List the proteins associated with sister chromatids during mitosis, and explain what happens
at the beginning of anaphase.

What happens if the spindle fibres are not properly attached during metaphase?
TOPIC 7 – INTRACELLULAR SIGNALLING AND TRANSPORT

TOPIC 7A. BIOCHEMICAL MESSENGERS

List and briefly describe 7 general components of cellular communication pathways.

What are the 4 main types of extracellular signalling molecules and how do they differ from
one another?

Nuclear receptors are a common type of intracellular receptors. What are the two main types
of nuclear receptor and how do they differ from one another?

List and briefly describe the three main classes of cell-surface receptors.
Describe the functions of molecular switches (kinases/GTPases) in signalling.

What are secondary messengers? List four examples.

Describe how epidermal growth factor (EGF) stimulates cell growth and signalling via the
Ras-MAPK pathway.

TOPIC 7B. CELL PROTEIN TRAFFICKING AND SECRETION

Outline how proteins with distinct localisation signals are delivered to the nucleus and
mitochondrion.

Briefly describe the steps involved producing a secreted protein.

Briefly describe the roles of coat proteins, Rabs, and SNAREs in protein trafficking and
secretion.

What is the difference between regulated and unregulated exocytosis in secretion?

TOPIC 8 – MEMBRANE TRANSPORT & ACTION POTENTIALS

TOPIC 8A. MEMBRANE TRANSPORT

Diffusion is the random movement of molecules down a concentration gradient. What does
“down a concentration gradient” mean?

Explain how solute molecular weight, lipid solubility and charge influence membrane
permeability.

Define the concept of flux and its relationship to membrane permeability.

How is diffusion of solutes through a membrane different from diffusion through a

pore/channel?

Define osmolarity, osmolality and tonicity.

TOPIC 8B. MEMBRANE TRANSPORT – PUMPS & CARRIERS
Describe how pores, channels and transporters increase cell membrane permeability.

List two major differences between a carrier protein and a pump.

Membrane transporters (carriers and pumps) show saturation. Explain.

Primary active transport directly uses an ATPase. What is an ATPase and why is it needed
for primary active transport?

Secondary active transport uses a co-transporter to move one substance down its
concentration gradient and another up its gradient. List and briefly describe two types of co-
transporter.

Active transport keeps the contents of cells far from equilibrium. Why is this important?
TOPIC 8C. SENSITIVE & SELF-SENSITIVE CELLS
Explain the ionic basis of membrane potentials.

What is the Nernst equation and how does it relate to the concept of electrochemical
equilibrium?

What is the Goldman equation and how does it relate to the steady state membrane
potential?

Describe and explain the ionic basis of electrical signalling in excitable (nerve and muscle)
cells.

Revise concept: The electrical response of “excitable cells” (receptors) depends on the type
of membrane transport processes present in those cells.
TOPIC 9 – APPLICATIONS OF MOLECULAR BIOLOGY

TOPIC 9A. MOLECULAR CELL BIOLOGY & DISEASE

Outline some of the major causes of molecular diseases.

Describe the molecular cause of malaria.

Describe the molecular cause of cystic fibrosis.

Describe the molecular cause of muscular dystrophies.

TOPIC 9B. MICROBIAL BIOTECHNOLOGY
Define biotechnology.

Describe the basic principles and uses of the following: bioremediation (natural and artificial),
biosensors, biopesticides/bioinsecticides, bioreactors.

List at least 5 major industrial products made by recombinant bacteria and their uses.

TOPIC 9C. GENETIC ENGINEERING OF PLANTS

Define a transgene.
List the properties of Agrobacterium tumefaciens that make it useful in generating transgenic
plants.

Describe a Ti plasmid and the properties that make it useful for genetically modifying plants.

Briefly describe the basic steps in regenerating a plant from transformed callus tissue.

Define sense and antisense plants.