BIOB11 EXAM REPORTED
QUESTIONS WITH COMPLETE
SOLUTIONS
Copy number polymorphisms (CNPs) - Answer- Differences in the number of copies of
a particular sequence
In protein coding region, extra copies = more protein -- phenotypic differences
Structural Variation - Answer- Segments of the genome can change, and these changes
may involve large segments of the DNA- duplication, inversion, deletion etc. that can
alter chromosome structure
mobile dna causes what - Answer- mutations
in bacteria and plants what is the occurance of transposition events - Answer- •In
bacteria, 1 transposition event occurs every ~105 divisions (rare or it would be deadly!)
•In plants and animals, transposition events are much more common (10-100 /
offspring)
Why can plants and animals survive a higher frequency of transposition events? -
Answer- •Transposition has played an important role in evolution by altering gene
sequences (exon shuffling) and regulatory sequences
•Some viruses have similar mechanisms for moving into host genomes and can
similarly be a source of genetic change
since we have giant genomes and lots of unimportant dna serves to protect us from
these events, as transposons jump around in our genome it is likely that they jump to
the unimportant dna so its more likely that we will not really differ from it - some wiggle
room when you are a multicellular organism - we can get messy without dna because
we can afford to
Its very easy to change things in organisms by changing or shuffling their genes, explain
how viruses can change as well - Answer- Viruses can bring in new sequences or pick
up dna and move them into organisms as well
Viruses and transposons are mechanisms for duplicating and reshuffling our genetic
sequences - Important because we make new genes out of old genes , all genes come
from somewhere
how do transposons cause genetic change - Answer- because sometimes these
transposons pick up extra sequences of dna
,Sometimes lines do not have a very strong end to transcribe the rna - meaning
sometimes we keep making rna past the line adding in some more sequences so that
entire part with the extra sequences can be inserted somewhere
Mobile dna - can also disrupt sequences separate genes from regulatory eleemnts or
land in the middle of exons or regukatory elements , these are mechanisms for many
types of mutations
paralogs = happening in ---- - Answer- parallel
are globin genes orthologs or paralogs or homologs - Answer- they are homologs -
common origin
true or false •Low error rate of DNA replication is essential for survival - Answer- true
are all snps bad for us - Answer- •Some SNPs are tolerable or even make
advantageous new alleles, but the majority of mutations in coding sequences would
have a negative impact (so must occur at LOW frequency)
how do keep a low error rate - Answer- •The existing DNA strand serves as a template,
and if an error disrupts complimentary base-pairing, then it is usually detected and
corrected
Separate catalytic sites for polymerization and editing: DNA is pushed into the editing
site when a mismatch is detected - we can sense when its not correct
- proof reading mechanisms - The Three Steps That Give Rise to High-Fidelity DNA
Synthesis - Answer- when we have 5 - 3 polymerization - Incorrect matches are harder
to covalently bind to the growing chain only 1 in 10 to the 5
3- 5 exonucleatic proofreading - DNA pol editing function clips off mismatched
nucleotides 1 in 100
strand directed miss match pair - iIdentifies mismatches after replication (by distorted
shape) 1 in a 1000
combined 1 in 10 to the 10
Strand-directed mismatch repair - Answer- •Occurs in both prokaryotes and eukaryotes
•Distortions of the double-helix are used for recognition of mismatched base-pairing
•Can distinguish which strand is newly synthesized and target that strand for correction
and uses the other strand as the template
•In both prokaryotes and eukaryotes mismatch repair involves:
1.Recognition of mismatch
2.Identification of newly synthesized strand
3.Removal of incorrect nucleotides from new strand
4.Resynthesis of excised segment (using other strand as template)
5.Ligation to seal DNA backbone
,LECTURE 7 STARTS HERE - what are the proposed models of dna replication -
Answer- Semi conserved - each strand becomes a template - so its one whole strand
and one new strand goes to one daughter strand and one to the other
Conservative - 2 original strands stay together and you make replicas of it but its of 2
new strands
Dispersive - maybe parent strands were broken into smaller pieces, synthesized and
then put back together - In dispersive replication model, parent strands are broken into
smaller fragments and used for daughter strand synthesis.
Fragments would then be joined to form complete strand of DNA
what do the proposed model experiments take advantage of - Answer- Experiment
takes advantage of the fact that some isotopes are heavier than the majority of isotypes
that exist - extra neutrons that Make a different structure
what is the actual model of dna - Answer- Semi-Conservative
explain the experiment that helped to find that dna was semi conservative - Answer-
Used 'heavy' and 'light' isotopes of nitrogen (15N and 14N respectively) --> incorporated
in DNA bases
•
•Ratio of heavy/light nitrogen determined the migration of DNA on CsCl gradient -->
more 15N will result in DNA being more dense
•More 14N will incorporated over time but the original 'heavy' DNA strands would still be
present.
When incorporated (the isotopes) it changes the strand
Next round of replication instead of having a heavy band and light band they have an in
between band which shows that the heavy strand and newly synthesized strand is both
mixed together basically , they are combined and so now theres a light band - hybrid
dna and one strand is old one is new , one with n14 one with n15
with the semi conservative experiment if it was dispersive or conservative what would
we see - Answer- If it was a dispersive we would see everything mixed
If it was conservative you would never see a heavy band you would only see n14 band
Dna replication is conservative, new dna in a cell is half old half new paired together in a
double helix
Experiment by separating by density showed us this
which way is dna always replicating , explain the replication - Answer- DNA Replication
is 5' to 3'
Incoming nucleoside triphosphate base pairs with the template strand and is then
covalently attached to the 3' OH
, The hydrolysis of the phosphate bond provides the energy to create this new bond
(Could NOT work if trying to extend the 5' phosphate
DNA polymerization MUST extend an existing 3'OH (strand grows in 5' to 3' direction)
How does the structure of DNA make replication possible? - Answer- Open up DNA
(make it single stranded) so that each individual strand can serve as template for
synthesis of complimentary new strand.
- Complimentary base-pairing allows the selection of the correct nucleotides to properly
replicate the sequence.
- Hydrogen bonds between bases allow DNA strands to be separated.
When dna is opened up each of the strands can serve as a template - so they have a
built in template model either of them can be used as a template
Complementary base pairing allows for it to be matched and replicated properly
Hydrogen bonding in between the strands allow the strands to be pulled apart, if they
couldn't be pulled apart then one of the strands couldn't be used as a template
what is denaturation and renaturation and how is it possible - Answer- •The ability of the
two DNA strands to unwind and separate into two individual strands is called
denaturation
•Complementary single stranded DNA molecules can re-associate (Renaturation or
Reannealing or Hybridization
This is possible because the double stranded (ds) DNA molecule (helix) is held together
by hydrogen bonds (weak and non-covalent) between the bases (complimentary base-
pairing)
Ability to reversibly make single-stranded DNA (and use it as a template) is critical for
transcription and DNA replication AND allows us to probe and synthesize DNA in the
lab
how can you have denaturation in a lab - Answer- In a lab setting you can break a
double helix into single strand by heat , you can use heat to break them apart -
denaturation - ability to take heat and turn it into single strand
how does base pairing help in renaturation - Answer- Renaturation - ability for them to
come back together they can find the base pairs and come back together
We can pull it apart and put them back tigetehr - hydrogen bonds to pull apart and the
complementary base pairs guide them to come back together
dna denaturation in detail - Answer- Experimentally when DNA is dissolved in a weak
saline solution and slowly warmed to a certain temperature DNA strand separation
begins. Within a few degrees (°C) of initiation of strand separation, the two chains are
QUESTIONS WITH COMPLETE
SOLUTIONS
Copy number polymorphisms (CNPs) - Answer- Differences in the number of copies of
a particular sequence
In protein coding region, extra copies = more protein -- phenotypic differences
Structural Variation - Answer- Segments of the genome can change, and these changes
may involve large segments of the DNA- duplication, inversion, deletion etc. that can
alter chromosome structure
mobile dna causes what - Answer- mutations
in bacteria and plants what is the occurance of transposition events - Answer- •In
bacteria, 1 transposition event occurs every ~105 divisions (rare or it would be deadly!)
•In plants and animals, transposition events are much more common (10-100 /
offspring)
Why can plants and animals survive a higher frequency of transposition events? -
Answer- •Transposition has played an important role in evolution by altering gene
sequences (exon shuffling) and regulatory sequences
•Some viruses have similar mechanisms for moving into host genomes and can
similarly be a source of genetic change
since we have giant genomes and lots of unimportant dna serves to protect us from
these events, as transposons jump around in our genome it is likely that they jump to
the unimportant dna so its more likely that we will not really differ from it - some wiggle
room when you are a multicellular organism - we can get messy without dna because
we can afford to
Its very easy to change things in organisms by changing or shuffling their genes, explain
how viruses can change as well - Answer- Viruses can bring in new sequences or pick
up dna and move them into organisms as well
Viruses and transposons are mechanisms for duplicating and reshuffling our genetic
sequences - Important because we make new genes out of old genes , all genes come
from somewhere
how do transposons cause genetic change - Answer- because sometimes these
transposons pick up extra sequences of dna
,Sometimes lines do not have a very strong end to transcribe the rna - meaning
sometimes we keep making rna past the line adding in some more sequences so that
entire part with the extra sequences can be inserted somewhere
Mobile dna - can also disrupt sequences separate genes from regulatory eleemnts or
land in the middle of exons or regukatory elements , these are mechanisms for many
types of mutations
paralogs = happening in ---- - Answer- parallel
are globin genes orthologs or paralogs or homologs - Answer- they are homologs -
common origin
true or false •Low error rate of DNA replication is essential for survival - Answer- true
are all snps bad for us - Answer- •Some SNPs are tolerable or even make
advantageous new alleles, but the majority of mutations in coding sequences would
have a negative impact (so must occur at LOW frequency)
how do keep a low error rate - Answer- •The existing DNA strand serves as a template,
and if an error disrupts complimentary base-pairing, then it is usually detected and
corrected
Separate catalytic sites for polymerization and editing: DNA is pushed into the editing
site when a mismatch is detected - we can sense when its not correct
- proof reading mechanisms - The Three Steps That Give Rise to High-Fidelity DNA
Synthesis - Answer- when we have 5 - 3 polymerization - Incorrect matches are harder
to covalently bind to the growing chain only 1 in 10 to the 5
3- 5 exonucleatic proofreading - DNA pol editing function clips off mismatched
nucleotides 1 in 100
strand directed miss match pair - iIdentifies mismatches after replication (by distorted
shape) 1 in a 1000
combined 1 in 10 to the 10
Strand-directed mismatch repair - Answer- •Occurs in both prokaryotes and eukaryotes
•Distortions of the double-helix are used for recognition of mismatched base-pairing
•Can distinguish which strand is newly synthesized and target that strand for correction
and uses the other strand as the template
•In both prokaryotes and eukaryotes mismatch repair involves:
1.Recognition of mismatch
2.Identification of newly synthesized strand
3.Removal of incorrect nucleotides from new strand
4.Resynthesis of excised segment (using other strand as template)
5.Ligation to seal DNA backbone
,LECTURE 7 STARTS HERE - what are the proposed models of dna replication -
Answer- Semi conserved - each strand becomes a template - so its one whole strand
and one new strand goes to one daughter strand and one to the other
Conservative - 2 original strands stay together and you make replicas of it but its of 2
new strands
Dispersive - maybe parent strands were broken into smaller pieces, synthesized and
then put back together - In dispersive replication model, parent strands are broken into
smaller fragments and used for daughter strand synthesis.
Fragments would then be joined to form complete strand of DNA
what do the proposed model experiments take advantage of - Answer- Experiment
takes advantage of the fact that some isotopes are heavier than the majority of isotypes
that exist - extra neutrons that Make a different structure
what is the actual model of dna - Answer- Semi-Conservative
explain the experiment that helped to find that dna was semi conservative - Answer-
Used 'heavy' and 'light' isotopes of nitrogen (15N and 14N respectively) --> incorporated
in DNA bases
•
•Ratio of heavy/light nitrogen determined the migration of DNA on CsCl gradient -->
more 15N will result in DNA being more dense
•More 14N will incorporated over time but the original 'heavy' DNA strands would still be
present.
When incorporated (the isotopes) it changes the strand
Next round of replication instead of having a heavy band and light band they have an in
between band which shows that the heavy strand and newly synthesized strand is both
mixed together basically , they are combined and so now theres a light band - hybrid
dna and one strand is old one is new , one with n14 one with n15
with the semi conservative experiment if it was dispersive or conservative what would
we see - Answer- If it was a dispersive we would see everything mixed
If it was conservative you would never see a heavy band you would only see n14 band
Dna replication is conservative, new dna in a cell is half old half new paired together in a
double helix
Experiment by separating by density showed us this
which way is dna always replicating , explain the replication - Answer- DNA Replication
is 5' to 3'
Incoming nucleoside triphosphate base pairs with the template strand and is then
covalently attached to the 3' OH
, The hydrolysis of the phosphate bond provides the energy to create this new bond
(Could NOT work if trying to extend the 5' phosphate
DNA polymerization MUST extend an existing 3'OH (strand grows in 5' to 3' direction)
How does the structure of DNA make replication possible? - Answer- Open up DNA
(make it single stranded) so that each individual strand can serve as template for
synthesis of complimentary new strand.
- Complimentary base-pairing allows the selection of the correct nucleotides to properly
replicate the sequence.
- Hydrogen bonds between bases allow DNA strands to be separated.
When dna is opened up each of the strands can serve as a template - so they have a
built in template model either of them can be used as a template
Complementary base pairing allows for it to be matched and replicated properly
Hydrogen bonding in between the strands allow the strands to be pulled apart, if they
couldn't be pulled apart then one of the strands couldn't be used as a template
what is denaturation and renaturation and how is it possible - Answer- •The ability of the
two DNA strands to unwind and separate into two individual strands is called
denaturation
•Complementary single stranded DNA molecules can re-associate (Renaturation or
Reannealing or Hybridization
This is possible because the double stranded (ds) DNA molecule (helix) is held together
by hydrogen bonds (weak and non-covalent) between the bases (complimentary base-
pairing)
Ability to reversibly make single-stranded DNA (and use it as a template) is critical for
transcription and DNA replication AND allows us to probe and synthesize DNA in the
lab
how can you have denaturation in a lab - Answer- In a lab setting you can break a
double helix into single strand by heat , you can use heat to break them apart -
denaturation - ability to take heat and turn it into single strand
how does base pairing help in renaturation - Answer- Renaturation - ability for them to
come back together they can find the base pairs and come back together
We can pull it apart and put them back tigetehr - hydrogen bonds to pull apart and the
complementary base pairs guide them to come back together
dna denaturation in detail - Answer- Experimentally when DNA is dissolved in a weak
saline solution and slowly warmed to a certain temperature DNA strand separation
begins. Within a few degrees (°C) of initiation of strand separation, the two chains are
