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Bio Info Flow Quiz
Terms in this set (17)
Be able to describe the structure of DNA and why its structure provides stability and fidelity.
Structure of DNA
The helix is "right-handed,"
are held together by hydrogen bonds
between the nitrogenous
bases, which are paired in the interior of the double helix.
Describe how DNA structure relates to how DNA is replicated, including nucleotide structure,
antiparallel orientation, complementary base pairing, and hydrogen bonding between the bases.
The two strands
are complementary; each stores the information necessary to
reconstruct the other.
Prior to replication, the strands unwind and hydrogen bonds are broken.
Double helix are antiparallel, meaning that they are oriented
in opposite directions to each other.
Two new strands formed during
DNA replication must also end up antiparallel to their template
Elongate from 5' tp 3'.
Draw a DNA replication fork, describe the proteins needed to carry out replication, and make a
new strand of DNA from a template using base pairing and directional rules.
Helicase - untwist double helix
Primase - starts the RNA chain, and parental DNA strand is used as template.
DNA polymerases - catalyze the synthesis
of new DNA by adding nucleotides to a preexisting chain. DNA polymerase III can synthesize a complementary
strand continuously by elongating the new DNA in the mandatory
5′→ 3′ direction. DNA polymerase I (DNA pol I), replaces
the RNA nucleotides of the adjacent primer with DNA nucleotides
DNA ligase - joins
Describe our current understanding of how DNA is replicated by the polymerase complex on
Because of their structure, DNA polymerases
can add nucleotides only to the free 3′ end of a primer or
growing DNA strand, never to the 5′ end. DNA pol III remains in the replication
fork on that template strand and continuously adds nucleotides
to the new complementary strand as the fork progresses - leading strand. The DNA strand elongating in this direction is called
the lagging strand - in segments (Okazaki fragments).
Describe the mechanisms of DNA proofreading and DNA mismatch repair, including steps in the
process and proteins involved and their roles.
polymerases proofread each nucleotide against its template
as soon as it is added to the growing strand.
In mismatch repair, other enzymes
remove and replace incorrectly paired nucleotides resulting
from replication errors.
1. Recognized by MutS protein, which is bound by MutL.
2. A kilobase away, MutH recognizes and binds to GATC site. This enzyme is a weak endonuclease and will create backbone incision. Enzyme recognizes new DNA bc it lacks methyl groups.
3. MutH is activated when bound by MutL which causes DNA to bend.
4. Exonuclease enzyme begins to excise DNA from the nick site created by Much. It excises DNA until just pass the mismatch.
5. DNA poly III begins to resynthesize the excised strand.
6. DNA ligase ligate the DNA backbone nick.
Describe the method used to repair DNA damaged by UV exposure.
1. Teams of enzymes detect
and repair damaged DNA,
such as this thymine dimer, which distorts
the DNA molecule.
2.A nuclease enzyme cuts
the damaged DNA strand at
two points, and the damaged
section is removed.
3. Repair synthesis by
a DNA polymerase
fills in the missing
4. DNA ligase seals the
free end of the new DNA
to the old DNA, making the
Identify the common features of single-stranded DNA repair mechanisms, including the enzymes
involved and their respective functions.
DNA proofreading fixes errors during replication. (DNA poly III back up and remove base pair).
DNA mismatch repair following replication. (MutL, MutH, and ligase).
Nucleotide excision repair fixes UV damage. (Nuclease removes thymine diner, Polymerase fixes sequence, and Ligase binds it).
Compare and contrast the two mechanisms used to repair double-stranded breaks in the
Repaired by either homology directed repair (HDR) or by non-homologous end joining (NHEJ).
HDR: has other strand to repair it from.
NHEJ: No template; not always going to work. Insertion or deletion.
Describe the mechanism of CRISPR/Cas 9 gene editing, and how naturally occurring DNA repair
mechanisms are related to this process.
CRISPR Components: Target Sequence, Cas9 enzyme, Guide RNA, and donor template if doing HDR.
1. Identify DNA sequence
2. Create specific guide RNA
3. Guide RNA is attached to Cas9
4. Introduced to target letter sequence and cuts the DNA
5. Editing by modifying, deleting, or inserting different sequences.
Distinguish between the outcomes of a HDR vs a NHEJ based CRISPR/Cas9 experiment when
addressing a research question or medical application.
HDR: Insert dominat gene to knock out recessive gene introduced by Cas9.
NHEJ: Knock out (frameshift).
Explain the role of cell cycle arrest and apoptosis in maintaining fidelity of genetic information.
Cell cycle arrest is a stopping point in the cell cycle, where it is no longer involved in the processes surrounding duplication and division.
Apoptosis is programmed cell death and it happens if repair does not work.
Accurately define the diploid state and be able to read a karyotype.
Diploid means two sets of chromosomes.
Define the role of each phase of the cell cycle and the cycle checkpoints.
Two major phases: Interphase - cell grows and copies its DNA - and mitotic (M) phase - form new cells.
G1 phase: cell grows
G0: resting state, not ready to divide
G1 Checkpoint: nutrients, growth signals, and DNA damage.
S phase: DNA replication
G2 phase: grows nice and preps for mitosis
G2 Checkpoint: Cell size and replication
M phase: divides copied DNA and cytoplasm to make two new cells. Four stages - prophase, metaphase, anaphase, and telophase.
Cytokinesis: Cell split into two
M Checkpoint: Chromosomes spindle attachment
Distinguish between the terms chromosome vs. chromatid; and duplicated vs. unduplicated
Chromosome: Packaged DNA molecules
Chromatid: copy of chromosome
Unduplicated: Made up of one molecule of DNA
Duplicated chromosome: Contains two identical chromosomes joined together
Determine if a chromosome has 1 or 2 chromatids at various stages of the cell cycle and mitosis;
and determine how many copies of a given gene present at different stages.
Before Interphase: Chromosomes - 46 Chromatids - 46
After Interphase: Chromosomes - 46 Chromatids - 92
During Mitosis: Chromosomes - 46 Chromatids - 92
After Mitosis: Chromosomes - 46 Chromatids - 46
Summarize how mitosis creates genetically identical cells, including how chromosomes are
faithfully pulled into separate daughter cells using microtubules.
Define and draw mitotic nondisjunction and aneuploidy.
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