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BSCI 170- Midterm Exam Guide - Comprehensive Notes for the exam ( 38 pages long!)


Department
Biological Sciences Program
Course Code
BSCI 170
Professor
Patty Shields
Study Guide
Midterm

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UMD
BSCI 170
MIDTERM EXAM
STUDY GUIDE

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BSCI170 Exam 4 Study Guide
Topic 10: DNA Structure and Replication
What are three main “parts” of a nucleotide?
o Nitrogenous base, phosphate group, sugar backbone
What are the four bases found in DNA? RNA?
o Adenine, Thymine (DNA)/ Uracil (RNA), Guanine, Cytosine
How do nucleotides differ in RNA and DNA
o A-U (RNA) vs A-T (DNA)
What are the main features of the Watson & Crick Model of DNA?
o Double Helix Structure, Sugar-phosphate backbone, Strict nucleotide base
pairing, antiparallel strands
Can you explain (in word and/or pictures) the double helix?
o Anti-Parallel Strands, Strict Base Pairing, Hydrogen Bond
Why are DNA strands in a double helix anti-parallel?
o because of their polarities, one strand is going 5’ to 3’ in different directions
What is meant by “semiconservative replication”?
o New helix is formed with one parent strand and one daughter strand
Where does DNA replication start? How does this differ between prokaryotes and
eukaryotes?
o Starts at origin of replication, eukaryotes have many because they are in a line and
prokaryotes have one because they are a circle
What property of DNA structure causes there to be leading and lagging strands?
o Antiparallel structure
What is meant by 5' and 3' ends of nucleic acid strands?
o 5' carbon has a phosphate group attached to it and the 3' carbon a hydroxyl group
Given a DNA sequence, can you determine the complement?
o Look at base pairs (A-T, G-C) and work in the reverse direction
Can you explain (in word and/or pictures) DNA replication? What enzymes/proteins are
required for it? What role do the different enzymes play?
o biological process of producing two identical replicas of DNA from one original
DNA molecule. DNA is made up of a double helix of two complementary strands
Can you list the proteins required for DNA replication and give their functions?
o Helicase: Breaking up the hydrogen bonds that hold the DNA base pairs together,
o Topoisomerase: It cuts the DNA strand and reseals them to relieve TORSIONAL
strain that builds up when the helicase keeps breaking hydrogen bonds
o Primase: Synthesizes RNA primer.
o DNA Pol III: Elongates the primer in a 5’ to 3’ direction.
o DNA Pol I: Replaces primer RNA nucleotides with DNA nucleotides.
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o DNA Ligase: This connects Okazaki Fragments together by forming
COVALENT bonds between fragments.
o Single Stranded Binding Protein: Stabilizes the DNA strands until it can be used
as a template.
o Initiator Proteins: They come together on the DNA helix and unwinds it to create
the replication bubble.
What are two limitations on DNA polymerase activity?
o can only synthesis in a 5’ to 3’ direction and require a 3’ primer for elongation
Why does one of the limitations above lead to DNA replication having a leading and a
lagging strand? Explain what is meant by discontinuous synthesis.
o Must be synthesized in a 5’ 3’ direction and DNA Pol III only moves that way
o Lagging strand is synthesized discontinuously because the DNA POL III must
continuously go back as helicase unwinds more of the helix and thus can only
synthesize the strand in segments called okazaki fragments that are later all bound
together by ligase
Watson and Crick described the structure of DNA, with the main features
- Antiparallel strands
- Sugar-phosphate backbone outside
- Strict base-pairing of nucleotides inside (A:T; C:G)
- Double helix
DNA replicates by semi-conservative replication, such that each parental strand from a
double helix is used as a template to make a daughter strand along its entire length. This
results in two double helices, each one having an “old” DNA strand paired with a “new”
DNA strand.
DNA replication involves a number of proteins that are required to unwind the double
helix and make new, complementary strands.
DNA replication starts at an origin, where the DNA double helix begins the process of
unwinding. A replication bubble forms, consisting of two replication forks that move
away from each other in opposite directions. As the bubble expands, and the forks move
further apart, the new daughter strands are replicated inside the bubble.
During replication, new bases assemble in correct order because they follow strict base-
pairing, mediated by hydrogen bonding. The way nucleotides orient when pairing results
in the anti-parallel strands of the DNA double helix.
The antiparallel structure of DNA is the underlying cause of the need for a lagging strand during
DNA replication. This is a result of DNA polymerases only being able to add nucleotides to the
3’-end of a growing polynucleotide, in effect making DNA replication unidirectional. This
means DNA pol III is always moving toward helicase and following the replication fork on the
leading strand, but moving the wrong way (away from fork) on the lagging strand. Each time
new template DNA is exposed along the lagging strand a new primer is made, starting a new
daughter strand, resulting in a series of Okazaki fragments
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