Transcript Answers - MrsPalffysAPBio2013

Target I
Explain the historical significance of the
following scientists’ contributions to the study
of DNA and utilize their data to support the
claim that DNA is the source of heritable
information: Griffith, Avery, Hershey/Chase,
Franklin/Wilkins, Watson/Crick
Covered by scientist jigsaw activity.
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Target II
Compare and contrast the
structure of a single nucleotide
(phosphate, nitrogen base, sugar)
from both DNA and RNA.
3 Main Differences
Target III
Describe the structure of DNA. Be
sure to use the following terms:
deoxyribose, nucleotide, hydrogen
bond, phosphodiester bond,
purine, pyrimidine, 5’, 3’, A, T, C,
G, and anti-parallel. You may be
asked to label a diagram.
Structure of a Nucleotide
• A nucleotide is composed of three parts:
– 5 carbon sugar: deoxyribose (DNA), ribose (RNA)
– Phosphate group: PO43– Nitrogenous base:
• Purine: double ring structure - Adenine & Guanine
• Pyrimidine: single ring structure - Cytosine & Thymine
• Phosphate is bonded to 5’ carbon of sugar
• Nitrogenous base is bonded to 1’ carbon
• Phosphodiester bonds join nucleotides
together in backbone: phosphate of a
nucleotide binds to sugar of next nucleotide
Structure of a Nucleotide
Nucleotide analysis of the DNA of a rat
revealed 12% of nucleotides are adenine.
Determine the percentage of GUANINE in
the rat genome.
What ‘rule’ allows you to answer the
problem above?... Chargaff’s Rule
Structure of a Nucleotide
Structure of a Nucleotide
Hydrogen
bonding
between
nucleotides
Structure of DNA
• DNA is composed of two separate, linear strings of
nucleotides that are antiparallel
 One strand is organized 5’ --> 3’
 Other strand is organized 3’ --> 5’
 DNA is described as a double helix
• Hydrogen bonds form between nitrogenous bases of
each strand to stabilize the helix
 A = T (2 hydrogen bonds)
 C G (3 hydrogen bonds)
 Sequence of nucleotides is significant b/c…
 How can nucleotide sequence be altered?
 How can nucleotide sequence be repaired?
Structure of DNA
Target IV
Compare and contrast the genome
structure and organization of
prokaryotes and eukaryotes.
h
5
a
Nucleotides
There are about 3.2 billion base pairs
(6.4 billion total nucleotides)
in the human genome
 Complementary pairing of A and T,
C and G
 Smallest Unit of DNA- the monomer
1
61
121
181
241
301
361
421
481
541
601
661
721
781
841
901
961
1021
1081
1141
1201
1261
1321
1381
1441
1501
1561
Nucleotides in the GAA gene
gcgcctgcgc
cgccggtcac
ggccagggcg
gggccgggtc
ttgtcgccgg
gtgacgcgaa
gaggctctgg
ctgtccaggc
gccgtctgcg
gatttcctgc
ccagctcacc
cgtcccagag
cctgacaagg
aagcaggggc
cccagctaca
cgtaccaccc
gagactgaga
cccttggaga
tccgaggagc
acgacggtgg
tcgcagtata
accaggatca
tctcaccctt
aacagcaatg
ggtgggatcc
tacctggacg
tgccgctggg
gggaggccgc
gtgacccgcc
cgcgtgcgcg
ggtggggcgg
ggccgcgggt
ggaccccggc
gcctgccgca
catctccaac
ccctcgtgtc
tggttccccg
agcagggagc
cagtgcccac
ccatcaccca
tgcagggagc
agctggagaa
ccaccttctt
accgcctcca
ccccgcgtgt
ccttcggggt
cgcccctgtt
tcacaggcct
ccctgtggaa
tctacctggc
ccatggatgt
tggatgtcta
ttgtgggata
gctactcctc
gtcacgtgac
tctgcgcgcc
gaggtgagcc
tcggctgccc
ggaggtcggg
cacctctagg
gctgacgggg
catgggagtg
cttggcaacc
agagctgagt
cagcagacca
acagtgcgac
ggaacagtgc
ccagatgggg
cctgagctcc
ccccaaggac
cttcacgatc
ccacagccgg
gatcgtgcac
ctttgcggac
cgccgagcac
ccgggacctt
gctggaggac
ggtcctgcag
catcttcctg
cccgttcatg
caccgctatc
ccaccgcggc
cccgggcacg
gggccggggc
gcgccggcct
gatgaggcag
ttctcctcgt
aaactgaggc
aggcacccgc
gctgcactcc
ggctcctccc
gggccccggg
gtccccccca
gaggcccgcg
cagccctggt
tctgaaatgg
atcctgaccc
aaagatccag
gcaccgtccc
cggcagctgg
cagttccttc
ctcagtcccc
gcgcccacgc
ggcgggtcgg
ccgagccctg
ggcccagagc
ccgccatact
acccgccagg
cccgccccgc
accccggagt
tgcggggctt
ctcagttggg
caggtaggac
ccgcccgttg
acggagcggg
cctgctccca
tggggcacat
cagtcctgga
atgcccaggc
acagccgctt
gctgctgcta
gcttcttccc
gctacacggc
tgcggctgga
ctaacaggcg
cactctacag
acggccgcgt
agctgtccac
tgatgctcag
ccggtgcgaa
cacacggggt
cccttagctg
ccaagagcgt
ggggcctggg
tggtggagaa
gacgagctcc
ctccgcgggc
ccctgagcgc
aaagctgagg
agtgacctcg
ttcagcgagg
cctgtaggag
ccggctcctg
cctactccat
ggagactcac
acaccccggc
cgattgcgcc
catccctgca
acccagctac
caccctgacc
cgtgatgatg
ctacgaggtg
cgtggagttc
gctgctgaac
ctcgctgccc
caccagctgg
cctctacggg
gttcctgcta
gaggtcgaca
ggtgcagcag
cttccacctg
catgaccagg
Nucleotides in the GAA gene
1621
1681
1741
1801
1861
1921
1981
2041
2101
2161
2221
2281
2341
2401
2461
2521
2581
2641
2701
2761
2821
2881
2941
gcccacttcc
ttcacgttca
ggcggccggc
agctacaggc
cagccgctga
acagccctgg
ggcatgtgga
cccaacaatg
gcggccacca
ctctacggcc
cgcccatttg
acgggggacg
tttaacctgc
tcagaggagc
cacaacagcc
gccatgagga
caccaggccc
gactctagca
ccagtgctcc
gacctgcaga
cgtgagccag
atcaacgtcc
acagagtccc
ccctggacgt
acaaggatgg
gctacatgat
cctacgacga
ttgggaaggt
cctggtggga
ttgacatgaa
agctggagaa
tctgtgcctc
tgaccgaagc
tgatctcccg
tgtggagctc
tgggggtgcc
tgtgtgtgcg
tgctcagtct
aggccctcac
acgtcgcggg
cctggactgt
aggccgggaa
cggtgccaat
ccatccacag
acctccgggc
gccagcagcc
ccaatggaac
cttccgggac
gatcgtggat
gggtctgcgg
atggcccggg
ggacatggtg
cgagccttcc
cccaccctac
cagccaccag
catcgcctcc
ctcgaccttt
ctgggagcag
tctggtcggg
ctggacccag
gccccaggag
cctgcgctac
ggagaccgtg
ggaccaccag
ggccgaagtg
agaggccctt
cgaggggcag
tgggtacatc
catggccctg
gacctggact
ttcccggcca
cctgccatca
aggggggttt
tccactgcct
gctgagttcc
aacttcatca
gtgcctgggg
tttctctcca
cacagggcgc
gctggccacg
ctcgcctcct
gccgacgtct
ctgggggcct
ccgtacagct
gcactcctcc
gcccggcccc
ctcctgtggg
actggctact
ggcagcctcc
tgggtgacgc
atccccctgc
gctgtggccc
acatggactc
tggtgcagga
gcagctcggg
tcatcaccaa
tccccgactt
atgaccaggt
gaggctctga
tggttggggg
cacactacaa
tggtgaaggc
gccgatacgc
ccgtgccaga
gcggcttcct
tctacccctt
tcagcgagcc
cccacctcta
tcttcctgga
gggaggccct
tccccttggg
cacccccacc
tgccggcccc
agggccctgg
tgaccaaggg
ccggagggac
gctgcaccag
ccctgccggg
cgagaccggc
caccaacccc
gcccttcgac
ggacggctgc
gaccctccag
cctgcacaac
tcgggggaca
cggccactgg
aatcctgcag
gggcaacacc
catgcggaac
ggcccagcag
cacactgttc
gttccccaag
gctcatcacc
cacatggtac
tgcagctccc
cctggacacc
cctcacaacc
tggagaggcc
3001
3061
3121
3181
3241
3301
3361
3421
3481
3541
3601
3661
3721
3781
3841
Nucleotides in the GAA gene
cgaggggagc
acacaggtca
agtgagggag
cagcaggtcc
gtcctggaca
ccgggcggag
tgtgcgggca
taaccattcc
aacgtgtcta
tctgtgttaa
ttagccaccc
ggggtatgca
cggctgccca
ttcacaggac
ggaatc
tgttctggga
tcttcctggc
ctggcctgca
tctccaacgg
tctgtgtctc
tgtgttagtc
gcagctgtgt
aagccgccgc
ggagagcttt
taagattgta
ccctccatct
cctgagctcc
gagggctgga
ttgggagatt
cgatggagag
caggaataac
gctgcagaag
tgtccctgtc
gctgttgatg
tctccagagg
gcgggcctgg
atcgcttgtt
ctccctagat
aggtttgccc
gttcccagca
tgcttcgcgc
tgcctgccgg
ctaaatctta
agcctggaag
acgatcgtga
gtgactgtcc
tccaacttca
ggagagcagt
gaggctggtt
gggttgcatg
tccacctcct
cgcactgtgg
tcctcacctg
ccggagaagg
ctgctgctct
tccccgagca
agtgcaatta
tgctggagcg
atgagctggt
tgggcgtggc
cctacagccc
ttctcgtcag
ccccagggaa
tgtcacctgg
gggccggggc
gccggggcct
ttgccggcat
gggtgctcag
gccccaacgc
agcctgggaa
ttttaataaa
aggggcctac
acgtgtgacc
cacggcgccc
cgacaccaag
ctggtgttag
gcagagcctg
agctgggcac
tctggccccc
ggagggctgc
gcgggtagta
gtggaggtgt
gaccgcttcc
ctcaggaaaa
aggggcattt
Gene
There are about 20,000 genes in the
entire human genome
 There are thousands of nucleotides
per gene.
 Ex: The GAA gene (which
codes for an enzyme) has 3846
nucleotides on one strand.
GAA Gene Map
Chromosome
 Chromosomes are all different sizes
and contain different numbers of
genes and nucleotides.
Each chromosome is one long
molecule of DNA
Ex: Chromosome 17 (where GAA is
Found) has 1726 genes and
81 million nucleotides
Chromosome 17 Map
Human Genome46 chromosomes (23 pairs)
Genome
 Represents ALL of the DNA present
in an organism (human)
 Found in every nucleus of every cell:
3.2 billion base pairs (nucleotides)
20,000 genes
46 chromosomes (23 pairs)
Eukaryotic Packaging
• Eukaryotic DNA is linear
• Chromosomes of DNA packaged during
interphase as chromatin
• Chromatin condenses (further coils and
folds) into chromosomes before mitosis
• On average, chromosomes contain 2 x 108
nucleotide pairs
• An ‘unpackaged’ chromosome of this size
would be 6cm long!
Eukaryotic Packaging
Histone proteins
contain large
amounts of
positivelycharged amino
acids. Why?
Histone protein
+ DNA called a
nucleosome!
Prokaryotic Packaging
• Prokaryotic DNA is circular
• Typically, one single chromosome in
nucleoid region and many smaller plasmids
floating in cytoplasm.
• No histones
• Fit inside cell via
“supercoiling”->
Targets V & VI
The “big picture” and details
regarding the process of DNA
Replication… see target sheet for
full details… all of this is covered
in great detail in the class notes
and giant drawing we constructed
together.
Replication of DNA
• Enzymes and special proteins
facilitate the replication of DNA
•When does DNA have to be replicated? WHY?
•Be sure to determine the role in DNA replication
for each of the following:
–DNA polymerase (I and III)
–DNA ligase
–Primase
–Helicase
–Topoisomerase
–Nuclease
–Telomerase
–Single strand binding protein
Replication of DNA
• Replication of DNA is semi-conservative…
•Replication begins at origins of replication
•Prokaryotes have only one origin of replication. Why?
•Eukaryotes have many origins. Why?
•Each origin of replication creates a replication
bubble with 2 replication forks
Replication of DNA
Replication of DNA
Replication of DNA
Replication of DNA
•DNA polymerase facilitates the creation of
complementary strands of DNA using original
strand as template
•Energy required to create polymer comes from
nucleoside triphosphates! (ATP, GTP, CTP, TTP)
Replication of DNA
•DNA polymerase only adds new nucleotides to the
3’ end of an existing nucleic acid.
•First, an RNA primer of ~10 nucleotides is
made by primase so that DNA polymerase has
something to attach to & can begin constructing a
new DNA strand
•Therefore, at a replication fork, the complementary
strands of DNA are not created at the same rate!
•The leading strand is built faster and in a
continuous manner (only one primer required)
•The lagging strand is built slower and creates
Okazaki fragments, each fragment has a primer
Topoisomerase
• Relieves tension of
helix by making a
cut, allowing it to
“spin” and “relax”,
then reconnects
broken strands
Telomeres &
Telomerase
• Telomeres protect the ends of chromosomes from
degradation
• Get shorter and shorter, disappearing after about 50
cell divisions (Hayflick Limit)
• Telomerase prevents shortening by adding TTAGGG
repeats to telomere end (3’), creates “immortal cell”,
only found in stem cells and cancer cells
CONCEPT GENERALIZATION: REPLICATION
DNA nucleotides
RNA nucleotides
Topoisomerase
DNA polymerase (III, I)
Helicase
Primase
Ligase
Leading strand/Lagging strand
Okazaki fragments
Replication fork/Replication bubble
Single stranded binding proteins
Orientation (5’ to 3’, 3’ to 5’)
Fill In the Blank (Directionality)
ALL ENZYMES MOVE IN A __________ DIRECTION ALONG THE TEMPLATE
STRAND.
ALL NUCLEIC ACID STRANDS ARE SYNTHESIZED IN A ________ DIRECTION.
THE LEADING STRAND IN REPLICATION IS THE ONE THAT PROCEEDS
_____________ INTO THE FORK.
THE LAGGING STRAND IN REPLICATION IS THE ONE THAT PROCEEDS
_____________ OUT OF THE FORK.
Fill In the Blank (Answers)
ALL ENZYMES MOVE IN A 3’ to 5’ DIRECTION ALONG THE TEMPLATE
STRAND.
ALL NUCLEIC ACID STRANDS ARE SYNTHESIZED IN A 5’ to 3’ DIRECTION.
THE LEADING STRAND IN REPLICATION IS THE ONE THAT PROCEEDS 3’ to 5’
INTO THE FORK.
THE LAGGING STRAND IN REPLICATION IS THE ONE THAT PROCEEDS 3’ to 5’
OUT OF THE FORK.
Target VII
Describe the process and
significance of errors in DNA
replication, DNA repair
mechanisms, and mutagens.
Covered by cancer article
readings and reading book (16.2).