AP ESSAY QUESTIONS: 16-20 - Heritage High School

hollandmercifulBiotechnology

Dec 11, 2012 (5 years and 26 days ago)

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AP ESSAY
ANSWERS
: 16
-
20

1. Information transfer is fundamental to all living organisms. For TWO of the following examples, explain in detail, how th
e transfer
of information is accomplished.


A) The genetic material in one eukaryotic cell is copied and di
stributed to two identical daughter cells.

B) A gene in a eukaryotic cell is transcribed and translated to produce a protein.

C) The genetic material from one bacterial cell enters another via transformation, transduction or

conjugation.

16

total pts poss
ible

A) max

8

pts combined (4 pts max each part


Part a is looking for “copy and distribute”)


“copy”= DNA replication



-
when DNA is copied
-

interphase, S phase of cell cycle



-
recognition of origin site on DNA



-
concept of unwinding enzyme (helicase)



-
RNA primer (RNA primase)



-
DNA polymerase
-

adds complementary nucleotides to DNA template strand



-
concept of complementary relationship among bases
-
semiconservative antiparallel backbones




and 5’
-
>

3’ generation of new segments



-
DNA ligase
-

hoo
ks Okazawki fragments together



-
Other
-

telomere replication, proofing by DNA polymerase


“distribute

=Mitosis



-
concept of chromatid pairs or doubled chromosomes



-
prophase
-

condensation of chromosomes, spindle formation



-
metaphase
-
alignment of chrom
osomes



-
anaphase
-

separation of chromatids or equivalent statement



-
telophase/cytokenesis
-

nuclear membrane reforms, division to two cells
-
cell plate or furrow,



-
other
-

cell cycle contro
l, cell surface area/volume ratio and mitosis

B) max 8

pts comb
i
ned (4

pts max each part
-

Part B is looking for transcription and translation


Transcription



-
functional definition
-

DNA sequence to RNA sequence



-
promoter recognition



-
RNA polymerase
-

adds complementary RNA nucleotides to DNA template



-
complement
ary relationships (T changes to U)



-
5’
-
>

3’
-

growth of new strand



-
start site/termination sequences



-
introns/exons with general explanation



-
caps/tails for mRNA processing



-
other
-

transcription factors, spliceosomes, enhancers


Translation



-
fun
ctional definition
-

mRNA base sequences to amino acids





inititation



-
sequence of events
-

complex includes mRNA, small unit of ribosome, first tRNA



-
structure of ribosomes
-

complete description
-

two subunits, 2 action sites, rRNA and proteins





Elongation



-
tRNA structure
-

amino
-
acyl (A) site and anticodon



-
complementary
-

codons to anticodons, mRNA base sequence to tRNA base sequence



-
peptide formation
-

amino acids joined together by peptide bonds to form polypeptide





Termina
tion



-
stop codon
&
release p
olypeptide +&
release ribosomes



-
other
-

triplet code, recognition segments, wobble (redundancy)

*one point can be granted to either section of part b for describing th
e movement of RNA from the
nucleus to the cytoplasm



C)
m
ax 8

pts
-

choose one only


Transformation



-
functional definition
-

uptake of naked DNA from environment into bacteria



-
competency
-

cell membrane permeable to fragments



-
how to make competent
-

Calcium chloride, heat shock, cold stability, gene gun, el
ectroporation



-
parameters for individual DNA segments
-

size, double helix



-
description of Griffiths/Avery expt
-

information transfer emphasis



-
other
-

recognition of transfer thru
gene technology, plasmid description, antibiotic resistance




(can get

2 pts for this)




Transduction



-
functional definition
-

viral vector (bacteriophage) that goes from bacteria to bacteria, transfers

bacterial DNA





(can get two points for this)



-
lytic cycle
-
describe, makes many copies of virus fast, released (can g
et two points for this)



-
lysogenic cycle
-

describe, incorporates viral DNA into bacterial DNA, replicates, reproduces




when induced, goes to lytic cycle (can get two points for this)



-
excision



-
other
-

prophage, oncogene, gene technology (can get t
wo points for this)


Conjugation



-
functional definition
-

direct contact between bacteria, exchange of genetic information



-
pili
-

“hook” from male bacteria to female bacteria creating a cytoplasmic bridge



-
F+ factor
-

donor(+), recipient (
-
)



-
Hfr cel
ls



-
replication of transferred segment



-
other
-

antibiotic resistance, plasmid, gene technology (can get two points for this)

_________________________________________________________________________________________




2. The human genome illustrates bo
th continuity and change.

A) Describe the essential features of TWO of the procedures/tec
hniques below. For each of the
procedures/techniques you describe,
explain how its application contributes to understanding genetics.



-
The use of a bacterial plasmi
d to clone and sequence a human gene



-
Polymerase Chain Reaction (PCR)



-
Restriction Fragment Length Polymorphism (RFLP) analysis

B) All humans are nearly identical genetically in coding sequences a
nd have many proteins that are
identical in structure an
d function.
Nevertheless, each human has a unique

DNA fingerprint. Explain this
apparent contradiction.


16 points possible

A) max
12

pts total (
6

pts for each part of the subquestions)


Describe= max 3 pts, 1 for each bullet Explain= max 3 pts, 1 for
each bullet



Describe plasmid cloning:




-
cut plasmid with restriction enzyme




-
cut/isolate human sequence with the corresponding restriction enzyme




-
mix/ anneal/ligate




-
introduce recombinant plasmid into bacteria




-
select recombinant bacteria
(ex.
a
ntibiotic resistance, fluorescence, reporter gene, etc)




-
bacteria reproduction used to amplify the sequence (PCR)




-
describe either degradative (Maxam
-
Gilbert) or dideoxy (Sanger) method to generate
f
ragments




-
electrophoresis to separate frag
ments




-
read the sequence



Explain the contribution of plasmid cloning




-
source of the DNA is immaterial to cloning




-
used to produce transgenic organisms




-
used to make human proteins (insulin, HGH)




-
understanding gene structure/regulation




-
comparative genomics




-
development of gene therapies




-
making a gene library




-
amplifying a particular sequence



Describe PCR




-
heat to separate DNA strands




-
add primers




-
cool to anneal




-
add polymerase and/or nucleotides




-
specificatio
n of heat stable (Taq) polymerase




-
description of thermocycling process




-
repetition of process



Explain PCR




-
allows amplification of very small samples




-
replicates/amplifies a defined region




-
can be automated to allow for faster expansion o
f knowledge




-
can be used for forensics
/ evolutionary
applications




-
can be used for diagnosis




Describe RFLP analysis




-
DNA sample cut with restriction enzyme(s)




-
Separation of fragments (electrophoresis)




-
description/elaboration of electro
phoresis (charge/size/apparatus)




-
visualize fragments (probes, dyes, blots)




-
compare fragment sizes/mobility




-
compare single and double digests (two or more restriction enzymes)




-
compare individuals/species/organisms/tissue samples



Explain RF
LP contribution




-
trace RFLP’s as genetic markers in families




-
diagnose disease/carriers/prenatal samples




-
prepare fingerprints (for forensics, etc)




-
order fragments for physical mapping




-
compare genomes of different species/evolutionary rela
tionships




-
locate the flanking regions of the gene/sequence




-
find mutations




-
individual bands can be used for further analysis




-
can determine presence of sequence without knowing its function

B) max 4 pts to explain the contradiction




Sources

of difference in DNA fingerprint




-
var
iation in non
-
coding material (
introns, spaces, minisatellites, junk, transposable

elements)




-
point mutations, small deletions, SNPs (single NT polymorphisms)




-
variable number of tandem repeats (VNTRs/STRs)



Recognition of differences




-
a small percentage difference of a very large genome results in a large number of

nucleotide differences




-
PCR
-
based fingerprinting: differences found by where primers anneal




-
variation in restriction enzyme cutting site
s



Similarities among proteins




-
redundancy in the code for amino acids




-
neutral/silent mutation does not alter the function of the protein

Caution
: no explanation points in A) without an attempted description of procedure



Order of procedure poin
ts is not important if they are logical and accurate



No credit for mutations leading to new phenotypes



Codons specify amino acids (not proteins)

__________________________________________________________________________________________


3. By usin
g the techniques of genetic engineering, scientists are able to modify genetic material so that a particular gene of interest

from one cell can be incorporated into a different cell.


A) Describe a procedure by which this can be done.


B) Explain the purpo
se of
each

step of your procedure.


C) Describe how you could determine whether the gene was successfully incorporated.


D) Describe an example of how gene transfer and incorporation hav
e been used in a biomedical or
commercial application.

16

points possi
ble

Max 8 pts
(1 pt for each step 1
-
4 Part A and 1 pt for each step 1
-
4 Part B)

1. A)

get restriction enzymes

B)
cut to get sticky ends; splice DNA to isolate plasmid with gene of interest

2. A) make a packaging/delivery system (vector=plasmid, virus) B) s
o gene can be delivered to specific site;

3. A) incorporating into cell B)

transformation (CaCl2, heat
-

change permeability (competence) of host; shock)


B cont’d) viral infection, ligase, covalently bond piece into host DNA, electroporation, PEG

4 El
aboration
-
appropriate and detailed extra description like controlled experimental design, explanation of electrophoresis or use of
radioactive/fluorescent probe

C) determine gene incorporation/expression
-
max
4

pts, no more than 1 pt for elaboration


-
not p
henotypic change alone (ex. antibiotic resistance
,

color change)


-
protein
(microarray)
assay for change in electrophoretic mobility


-
reporter genes sequencing


-
nuclei acid hybridization
-

description is worth 3 pts max


elaboration
-

detailed explanat
ion of how, why it works, etc/ex.dideoxynucleotide method of gene sequencing

D) application
-

max
4

pts
-

must have description
-

not just name
, no more than
3

pt
s

for elaboration


-
transgenic animal


-
herbicide resistance


-
antibodies
/

growth hormone


-
gene

therapy (specific) ex. insulin production making clotting factor


elaboration
-
not just second example: explanation of

importance, how it is done, etc

4. Genes are located on chromosomes and are the basic unit of heredity that is passed on from parent
to child, through generations,

A) Explain how a chromosome mutation could occur and why mutations are detrimental to the organism in which they take place.

B) Explain why it is that
-
although there are very few genes located on the Y chromosome
-

human males

may suffer from having just
one copy of the X chromosome, whereas females have two.

12 pts possible

A) Max 6 pts (3pts for how mutation could occur, 3 pts for why detrimental)


-
Mutations



-
nondisjunction
-

improper splitting of chromosomes during meiosi
s/mitosis, one cell gets two, other gets none




-
aneuploidy



-
deletions (lose part of chromosome)



-
inversion
-
chromosome segment reversed within a chromosome



-
duplication
-

chromosome segment is repeated



-
translocation
-

part of chromosome is moved to

another chromosome


-

Abnormal chromosome
have
s

genes that code for proteins with specific functions



-
If organism has two copies of a particular gene, gene transcribed twice creating twice the usual gene product




-
alters doses of products
-
> serious d
evelopmental problems



-
If gene is missing from chromosome, won’t be transcribed and corresponding protein won’t be made




-
if protein has impt cellular function
-
> serious impact

B) Max 6 pts


-
Males
can

express all genes on the X chromosome because the
ir Y does not
contain complementary genes


-
Males can express all genes on their Y chromosome because their X chromosome does not contains complementary genes


-
Females have 2 copies of the X gene although one chromosome in each cell condenses into an inac
tive X called a Barr body


-
Because different cells in the female will have different X chromosomes deactivated, some cells will have the X




chromosome from mom activated and some will have the X chromosome from dad activated



-
this creates a blend of
activated cells with chromosomes from both parents (50
-
50 ratio)



-
ensures all necessary proteins are produced







































______________________________________________________________________________________


4. The diagram be
low shows a segment of DNA with a total length of 4900 base pairs. The arrows indicate reaction sites for
restriction enzymes (enzyme X and enzyme Y).


_____________________________________________________________________________



A) Explain how the princ
ipl
es of gel electrophoresis allow

for the separation of DNA fragments.


B) Describe the results you would expect from the electrophoresis separation of fragments from the following treatments of
the DNA segment above. Assume that the digestions (site of a
ttack by the restriction enzymes) occurred under appropriate conditions
and went to completion.



I. DNA digested with only enzyme X



II. DNA digested with only enzyme Y



III. DNA digested with both enzyme X and Y



IV. Undigested DNA


C) Explain both

of the following:



A) The mechanism of action of restriction enzymes



B) The different results you would expect if a mutation occurred at the recognition site for



enzyme Y.

16 points possible

A) max 4 pts


-
electricity…electrical potential (charge, f
ield) moves fragments


-
charge…negatively charged fragments move toward (+) anode through gel/(
-
) charge due to P groups


-
rate/size…smaller fragments move faster (farther) relative to lgr fragments. Describe logarithmic



relationship


-
calibration…DNAs o
f known molecular weights are used as markers/standards


-
resolution…depends on concentration of gel; is determined by pore size



-
apparatus…DNA is stained for visualization of bands/ explains use of wells, gel material, tracking dye,



buffers

B)
max 4
pts



-
Treatment I

(X only)
= 4 bands



-
Treatment II( Y only)
=
2 bands



-
Treatment III (X and Y )= 5 bands



-
Treatment IV (undigested)= 1 band

C)

max 4 pts for each C1 and C2
-



1.

-
recognition…binding of enzyme to target sequence/speci
fic short bp sequences of double




stranded DNA are targeted/recognizes specific targets 4
-
8 bp long/ site may be





palindromic



-
cutting…enzyme cuts at every target location/ may cut frequently or rarely



alternate
-

1 pt may be given if i
nstead of the above it is clear that the student says that the enzyme cuts at



a specific point


-
detail point…fragment lengths correspond to lengths between cutting sites
/ may generate blunt or



sticky ends



…methylation or modification



…breaks the
phosphodiester bond/describes mechanism in living systems



…restriction site may function as a genetic marker


2.

-
change in II…uncut/ 1 band ( looks like IV)


-
change in III…like I/ 2 bands


alternate
-


1 pt may be given instead of the above
if it is clear that the student says theat the Y sequence is



no longer recognized and cut.


-
detail point….describes that RFLPs (markers) might correlate with phenotypic variation



…Y site might become an X site



…deletion/insertion at Y site/ changes

fragment size



…silent alteration: (pyrimidine
-
>pyrimidine or purine
-
>purine in some target sequence

--
for 10 pts on question must have at least 1 pt from each section in part C