Bio99B Study Guide: Boiko half of the course

Textbook: Molecular Biology: Principles and Practice, by Cox, Doudna,

ODonnell, either full or custom edition (from last year)
Please visit our Website for all of the materials available for your use
The sitting chart will be posted before the exam on the website
There will be very few if any multiple-choice questions this year and most of the
questions require problem-solving skills, which we developed during our lectures,
along with the molecular biology language you learned.
Study strategy:
Follow class notes; re-read the material you highlighted in pre-lecture reading
assignments; follow the notes you took during the discussion sessions.
Most importantly (as I pointed out in class) you should be able to:

Know differences between RNA and DNA building blocks (dNTPs, dNMPs, NTPs,
NMPs) and know what is on the 5 and 3 ends of a monomer and how the
polymer looks like.
Know what 5 and 3 mean for DNA polarity and for the activity of the enzymes
operating on nucleic acids (e.g. 53 activity of DNA polymerase etc.)
Draw the 5 common bases, nucleosides and nucleotides structure and correct
nomenclature with numbering (including nomenclature for base alone or as part
of nucleotide). I am allowing you to have these in a one-page summary note.
Know Central Dogma and Exceptions
Know how deamination, oxidation, alkylation affects structure of nucleotides;
what groups get modified and what are the consequences for the double-helix
Know the chemistry of phosphodiester bond formation and breakage
What conditions stabilize the DNA helix and what destabilize it (salt, temperature,
pH, GC content)
Nucleic acid hybridization: know principle, probe design, what conditions affect
the outcome of hybridization experiment
Define Tm and use it in experiments
Know Frederick Griffiths and Oswald Averys transformation experiments
Know Hershey/Chase experiment
Know Genome content, simple sequence repeats
Define what gene is, how alternative splicing leads to one gene encoding for
several proteins
Being able to explain chromosome packaging, nuclease experiment
Being able to experimentally validate chromosome components (Murrays

experiment): ORI, Centromere, Telomere

Explain Meselson/Stahl experiment
Know diffreneces between Polymerisation-Pyrophosphorolysis-Proofreading
Know Lagging vs leading strand concept, small bubble, large bubble, trombone
model
Diagram steps in DNA synthesis, replication termination
PCR: primer design for acquisition of a particular product, being able to diagram
several cycles with primers annealed and extended
Knowing what the linking number is is not required, but you need to know what
overwound and underwound DNA is and how it affects replication/transcription,
as well as how topoisomerases contribute to this
Diagram Pre-RC, RC, details not important
Be able to explain the end replication problem and how to solve it, diagram
several rounds of replication and point out where the DNA gets lost
For the enzymes involved in phosphodiester bond formation and breakage
please pay attention to energy of the reaction in terms of ATP and dNTPs
I introduced you to the triplet genetic code used for translation, understanding it
is important for understanding insertion and deletion mutations
Being able to define mutation
Being able to design an Ames test for the compounds you are testing for
mutagenicity and analyze the data
In mismatch repair you need to know how cell distinguishes between parental
and daughter strands to conduct repair in prokaryotes and eukaryotes
Please pay attention to the cell cycle phase: each type of DNA repair is cell
phase specific
Know what is the genetic basis of XP, and explain the consequences at cellular
and organism level
Being able to diagram how a single strand break can potentially become a
double-strand break (replication fork collapse)
Being able to diagram what happens in the five types of DNA repair we
discussed (mismatch, BER, NER, HR, NHEJ)
Know what positive and negative controls are (see H.pilori experiment)
Know how to design a gene knockout cassette and how the technique works
We are using selection markers, ori, transformation, selection media throughout
the course, its important to learn that and be able to use the knowledge for
solving the problems
Genomic library vs cDNA library, DNA Sequencing and Complementation will be
included in the cumulative final, not in the midterm!

Being able to follow the experiments we analyzed in class. Play with

experimental conditions at home, its the best way to prepare for solving
the problems (change the selection marker and see how it will affect your
choice for selection media etc.)
2

Take a look at the Learning Goals before each lecture and ask yourself if
you achieved those
Take a look at the topics listed at the first slide of each lecture, you should
know these
Learn your molecular biology language well: know the difference between
telomere and telomerase, antibiotic and gene of antibiotic resistance,
adenine and gene for adenine synthesis etc.
These are just the highlights any topic covered in class/book can be
included on the exam.
Since the discussion sections were designed to reinforce the lecture
material, I will not include any questions directly from the Discussion
sections, which were not covered in the class.