Ch3 Study Guide and Practice Questions

Read all sections of Chapter 3. I covered most of Ch3 contents in lecture. You do not have
to memorize chemical structures of nucleotides. Reviewing Core Concepts Summary
and Self-Assessment at the end of each chapter are great tools to go with this study guide.

Key concepts to grasp

The Central Dogma of Molecular Biology

Please know that this is a general framework, but there are many exceptions to the
central dogma (e.g. not all RNA becomes protein, replication)
DNA is the genetic material
Understand how this was determined through experimentation (How Do We Know
Exercise).
DNA structure and replication
Double helix structure, antiparallel configuration (how is this DNA molecule stabilized?)
Complementary base pairing
The 5’ to 3’ direction of strand synthesis, writing DNA (and RNA) sequence in the 5’ to
3’ direction
The semiconservative nature of DNA replication
DNA vs. RNA
Difference between deoxyribose and ribose sugars
T vs. U nitrogenous bases
Double strand vs Single Strand
Long vs Short
Transcription
template strand and nontemplate strand
the 5’ to 3’ direction of strand synthesis
the function of the terminator, promoter and enhancer region of DNA
the function of RNA polymerase II
Transcription - Prokaryotes vs. Eukaryotes (differences)
Initiation of transcription (pro- sigma factor; euk, general and specific transcription
factors, enhancer region of DNA)
Eukaryote- RNA transcripts contain introns and exons; Prokaryote – RNA transcripts
do not contain introns
modification and processing of the primary transcript in eukaryotes, “regular” splicing
and alternative splicing, 5’cap and polyA tail

Practice Questions:

Q1: In the classic experiments performed by Avery, MacLeod, and McCarty (How Do We
Know Exercise), how would you expect the results of their experiment to differ if Protein
was actually the biomolecule that carried genetic material. (Please know this is an exercise,
and fictional!)
Q2: There is a eukaryotic gene called LYNX. It has four exons (A, C, E, and G) and three
introns (B, D and F). If exons A and G cannot be removed, how many proteins can
potentially be made from this primary transcript? Which exons are in each mRNA?

Q3: In a laboratory exercise you conduct transcription of a eukaryotic gene in a test tube.
Your lab teacher gave your group a secret test-tube transcription cocktail mix. Then, she
gave you two DNA fragments, both of which contain the LYNX gene (the entire gene or a
part of it). One fragment was longer than the other. When your lab group added the first
fragment (longer fragment) to the secret transcription mix, they successfully synthesized
many complete LYNX gene mRNA. However, when they added the other, shorter fragment
to the cocktail mix, they got very few complete LYNX mRNA and no incomplete mRNA.
What statement best explains the above observation?

a) The
shorter DNA fragment does not have a terminator sequence.
b) The
shorter DNA fragment does not have two intron sequences.
c) The
shorter DNA fragment does not have a promoter sequence.
d) The
shorter DNA fragment does not have enhancer sequences.

Q4: (A hypothetical) The same gene exists in E. coli (prokaryote) and in yeast (eukaryote).
The speed of transcription of any genes in E. coli and yeast is the same. However,
accumulation of the protein from this gene in E. coli occurs much faster than the protein
from this gene in yeast. What may explain this observation?