Download Chapters 12 through 16 Unit objective answers checked

Ms. Sastry
AP Biology
Leigh High School
Unit 3 – Genetics and Molecular Biology (Chp 12 to 16)
Checked and approved by your instructor – use to compare answers/study for final.
Chapter 12 – Mitosis Objectives:
1) What loses heat faster – an elephant or a mouse? Why?
A mouse will lose heat faster because it has a smaller volume to surface area ratio.
2) Why do cells divide?
Cells divide in order to maintain a small volume to surface area ratio. This ensures that
the cells are efficient in transporting nutrients and ridding itself of waste.
3) What is mitosis? When do cells undergo mitosis?
Mitosis is the process by which the cells divide. A cell will undergo mitosis when it is
signaled to by its surrounding and has reached the sufficient size to do so.
4) What are somatic cells? How many chromosomes do they contain? Do they undergo
mitosis?
Somatic cells are cells in a multicellular organism that are not sex cells. They contain the
normal amount of chromosomes in that particular organism. For example, the normal
human contains 46 chromosomes. These cells undergo mitosis.
5) What are gametes? How many chromosomes do they contain? Do they undergo mitosis?
Gametes are sex cells- sperm or ova. Each contains half the number of chromosomes that
are in the somatic cells. Gametes do not undergo mitosis in humans.
6) What are chromosomes – why are they important for mitosis?
Chromosomes are the condensed DNA strands present during mitosis. The DNA would
be unmanageable during mitosis if it did not condense.
7) What are genes? What is the genome?
Genes are the parts of the DNA that code for proteins. The genome is the complete length
of genetic material in the cell.
8) Describe the ultra-structure of the chromosome (include definitions for chromatin,
chromosome, beads on a string, histone and nonhistones). Make a quick sketch of how
DNA is folded to make chromosomes.
chromatin- uncondensed DNA, contained inside the nuclear envelope
chromosome- condensed DNA present during mitosis and meiosis
histone- a protein containing a high proportion of positively charged amino acids which
binds to negatively charged DNA to hold it in its chromatin structure
nonhistone- proteins that loop DNA together to create the chromosome structure
Ms. Sastry
AP Biology
Leigh High School
9) What are sister chromatids? Draw them. What structure connects the two sister
chromatids?
Sister chromatids are identical chromosomes present in the cell after DNA replication.
During mitosis, a centromere connects the two sister chromatids.
X
10) What is DNA replication and how does it relate to sister chromatids?
DNA replication copies the DNA so that there are two identical copies in the cell. Sister
chromatids are identical copies of the same segment of DNA and are the result of DNA
replication.
11) Why should DNA or chromosome replicate/duplicate itself? When does this happen
during the cell cycle?
The DNA replicates itself so that the genetic information is present in both daughter cells.
This happens during the S phase of interphase.
12) What is cytokinesis – when does it occur?
Cytokinesis is the division of the cytoplasm. It occurs at the end of telophase, the cell
cycle phase following mitosis.
13) What are the cell cycle phases? Use this cell cycle website to review it.
http://mama.uchsc.edu/vc/cancer/cellcycle/p1.cfm
The cell phases are interphase, prophase, metaphase, anaphase, telophase, cytokinesis.
Interphase is broken into three parts: G1, S, G2.
14) Using the above cell cycle website and the Sci. Am article – ‘How Cancer Arises’ write
an essay detailing how regulation of the cell cycle occurs and the consequences of the
failure in the checkpoints of the cell cycle.
Enzymes called kinases regulate cell division in conjunction with proteins such as
cyclins. These proteins are dependent on the kinase enzyme to become phosphorylated
thus, activating/deactivating them. There are several checkpoints during the cell cycle
that ensure the proper replication, alignment, distribution of genetic material to the
daughter cells. When these checkpoints are transgressed, abnormalities result such as
aneuploidy/cancer.
15) How long does a cell spend in the mitosis phase? How long does it spend in interphase?
The cell spends about 90% of its time in interphase, so 10% of its time is in the mitosis
phase.
16) What are the three phases of interphase? Describe what happens during each one.
The three phases of interphase are G1 (gap 1), S, G2 (gap 2). During gap 1, the cell grows
in size and it is also making protein and other factors needed for DNA replication. S
phase is all about replicating DNA. G2 phase – organelles are dividing and more growth
and protein synthesis before mitosis.
17) How many chromosomes do we have in each of our cells? Why do we have 2 sets of
each chromosome even in G1 phase, before replication of DNA? So, how many
chromosomes will we have then after S phase?
G1- 23 chromosomes come from the mother, and 23 from the father, which together form
the 23 pairs. Because the sister chromatids are attached after replication, we will still
have 23 pairs of chromosomes in the cell after the S phase. For a brief time during
Anaphase and Telophase we will have double the number of chromosomes – 46 pairs and
the original condition – 23 pairs is restored when cytokinesis occurs.
18) Describe what happens during the different phases of Mitosis.
Ms. Sastry
AP Biology
Leigh High School
(Website - http://www.loci.wisc.edu/outreach/bioclips/CDBio.html)
Interphase- cell growth, DNA replication
Prophase- condensation of chromatin (forms chromosomes), nuclear membrane disappears
Metaphase- chromosomes line up at center of the cell (metaphase plate)
Anaphase- separates sister chromatids
Telophase- two nuclear membranes form (one for each daughter cell), cytokinesis occurs
19) Compare plant and animal cell mitosis.
Plants form a cell plate, animal cells do not (cleavage furrow and actin filaments).
Animal cells contain centrioles, plant cells do not.
20) Describe how the mitotic spindle is formed and used to pull the chromosomes apart.
The mitotic spindle is made of many subunits of microtubules (specifically tubulin)
combined. Subunits assemble and disassemble to pull chromosomes apart. The
microtubules disassemble on the side towards the centrioles and the spindle fibers appear
to reel in the chromatids to the respective poles.
Chapter 13 – Meiosis Cell Division Objectives:
1) Define heredity and variation.
heredity- process of passing on genes
variation- genetic variations that result in different phenotypes, essential for evolution
2) What is a karyotype?
A karyotype is a map of an individual’s chromosomes. It is derived from the mitotic
chromosomes.
3) Where did you get your 23 pairs of chromosomes from?
23 chromosomes come from the mother, and 23 from the father, which together form the
23 pairs.
4) How many chromosomes does your gamete/germ cell contain?
The gamete/germ cell contains 23 chromosomes.
5) Why is sexual reproduction a price to pay compared to asexual reproduction? What are
the returns/benefits of going SEXUAL?
In sexual reproduction, the individual only passes on half of their chromosomes, while
asexual reproduction results in exact clones. The advantage is more variation.
6) Explain the terms – haploid and diploid.
Haploid – set of single chromosome
Diploid – set of duplicate chromosomes
7) What are homologous chromosomes? Are they the same as sister chromatids? Why or
why not?
They are pairs of chromosomes from both parents. They are not the same; sister
chromatids are exact copies of a single chromosome and homologous chromosomes are a
pair that code for the same trait but are not the same.
8) How many sets of homologous chromosomes do you have?
23
9) What happens to the homologous chromosomes during meiosis?
Ripped apart during meiosis 1
10) Review question - What happened to the sister chromatids during mitosis? Will this
happen in meiosis at some point? When?
Ms. Sastry
AP Biology
Leigh High School
The sister chromatids are taken apart in anaphase in mitosis. They will come apart during
meiosis 2
11) What is reduction division – why is meiosis considered as such? In comparison, what is
mitosis referred to as?
Gametes end up with less chromosomes than they started with so reduction division.
Mitosis is equation division.
12) Will the organism change from diploid to haploid after meiosis? Why or why not?
The gamete cell (not organism) is haploid. They are haploid because they must pair with
the mates’ chromosomes when they form the zygote.
13) Describe how Prophase I of meiosis causes the genes from the homologous chromosome
pairs to get mixed up. What is this called? (Define tetrad, chiasmata, synapsis)
It is called crossing over
tetrad: homologous chromosome held together
chiasmata: crossing over
synapsis: held together to form tetrads
14) Compare Metaphase I with Metaphase II. Do the same for the remaining phases of
Meiosis.
1: homologous line up; in 2 it’s the sister chromatids. (metaphase)
in 1 homologous break up; in 2 sisters break up. (anaphase)
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
15) How do crossing over, independent
assortment and random fertilization
contribute to the diversity and variation among the offspring produced?
Crossing over occurs in Prophase of meiosis I and it leads to the mixing of alleles on
homologous chromosomes. Independent assortment occurs due to there being multiple
Ms. Sastry
AP Biology
Leigh High School
ways of aligning different sets of chromosomes along the metaphase plate during Meiosis
I and II – leading to a mixing of traits inherited on separate chromosomes. Random
fertilization causes the union of any sperm with any egg that may e produced leading to
more variation. They introduce variations by mixing and matching – more details in
powerpoint (important question).
16) Do the G1, S, and G2 phase occur before meiosis?
Yes. But S phase occurs only once and 2 divisions take place therefore chromosome
number is halved at the end of meiosis.
Chapter 14 – Mendelian Genetics and beyond - Objectives:
1) What are traits?
Traits are the physical features that can be seen on an organism.
2) Define the following:
a) Phenotype – trait/feature seen on an organism.
b) Genotype – genetic make up of an individual for a given phenotype.
c) Alleles – 2 alleles = a trait; describe the different genes.
d) Homozygous – have two of the same alleles, either recessive or dominant.
e) Heterozygous – having two different alleles, one dominant and one recessive trait.
f) Dominant – allele that is fully expressed in a heterozygote.
g) Recessive – allele that is masked in a heterozygote.
h) True breeding – always producing offspring with the same traits as the parents, when the
parent plants are self-fertilized.
3) Draw Punnett squares and illustrate the following crosses:
a) Monohybrid Cross:
A
a
A AA Aa
a
Aa
aa
b) Dihybrid Cross:
AB
Ab
AB AA BB
AA Bb
Ab
aB
Aa BB
ab
AaBb
AB
AA Bb
Aa BB
AA bb
Aa Bb
Aa Bb
aa BB
Aa bb
aa Bb
ab
Aa Bb
Aa bb
aa Bb
aa bb
c) Test or Back Cross: one individual has to be homozygous recessive.
D
d
Dd
dd
d
d
dd
dd
Ms. Sastry
AP Biology
Leigh High School
4) State and prove Mendel’s Law of Segregation using an example
Alleles (A and a) separate in meiosis (gamete formation) since homologous
chromosomes are separated. They separate in Meiosis I. The alleles separate in this “law”.
An example would be a flower (Aa) whose chromosomes separated in meiosis to become the
gametes A, A, a, and a.
5) State and prove Mendel’s Law of Independent Assortment using an example
This is when there are 2 or more allele pairs, and each pair of alleles segregates into
gametes independently. There are at least two traits being looked at, as in a dihybrid cross but
the alleles are on different chromosomes with no crossing over. An example would be a
dihybrid cross between color (Aa) and height (Bb) in mice. The resulting gametes would be
AB, ab, Ab, and Ba.
6) Illustrate rule of multiplication and rule of addition with examples
The rule of multiplication – the chance that two or more independent events will occur
together. First you compute the probability that it will occur, then multiply them together.
For example, the probability of a heterozygous pea plant (Aa) of producing a recessive
offspring (aa) is 1/2 x 1/2 = 1/4. The rule of addition - the probability of an event that can
occur two or more different ways is the sum of the separate probabilities of those ways. For
example, the probability of a heterozygote in a monohybrid is 1/4 + 1/4 = ½ because you can
get the allele from mom or dad (2 ways for same event and only one occurs).
7) Explain the following exceptions to Mendelian rules with examples:
a) Incomplete Dominance – heterozygotes show a distinct intermediate phenotype.
I.e. – Purple (AA), Blue (Aa), Green (aa).
b) Codominance – two alleles affect the phenotype in separate, distinguishable ways.
I.e. – a flower is both purple and white.
c) Pleiotropy – affecting more than one phenotypic character. I.e. – missing protein
in blood cells results in sickle cell anemia with many other complications.
d) Epistasis – one gene alters another genes phenotypic expression. I.e. – B = dark
hair, b = light hair; BB, Bb = dark hair; bb = light hair.
e) Quantitative characters – traits depending on how many genes are expressed. I.e.
– Skin color has three genes to express color; from darkest to lightest: AABBCC,
AaBBCC, AABbCC, AABBCc, AaBbCc, aaBBCC, AabbCC, AABBcc.
f) Environmental effects on phenotype – Nature versus nurture. I.e. – the
surrounding environment affects how organisms look, along with their genetics.
8) How does a genotype determine the phenotype?
The genotype is the make up of genes, so depending on how the recessive and dominant
genes are assorted and combined shows through in the phenotype (physically). I.e. –
Genotype: BB, Bb, bb; Phenotype: Dark, dark, light. The genes code for proteins that may
be directly expressed as the phenotype ( example blood groups), OR it codes for an enzyme
that regulates a pathway leading up to a phenotype – example - skin color and melanin
production/deposition.
9) What does DOMINANCE mean in the above context?
Dominance is the allele that is expressed fully, even in a heterozygous genotype. So it
allow for that protein to be synthesized. Even if there is one copy of that gene, the protein is
still made and expressed normally in most cases except in codominance/incomplete
dominance.
10) How are human blood groups inherited? Do they follow Mendelian rules?
Ms. Sastry
AP Biology
Leigh High School
Human blood groups are inherited with half from mom and half from dad. It does follow
Mendelian rules for the I and i alleles, but not for the A and B alleles (codominance).
IAIA or IAi = A blood group
IBIB or IBi = B blood group
ii
= O blood group
IAIB
= AB blood group
11) What is a pedigree? How is it used?
A pedigree is a map out of family traits and it predicts phenotypes. It shows the genes of
family members and that information is used to guess which phenotype a child will inherit.
12) What are some methods of genetic screening to determine abnormalities in the unborn
fetus?
Amniocentesis is where some of the amniotic fluid is extracted from the mother’s
abdomen to test it for genetic abnormalities. Chorionic villus sampling (CVS) is when a
catheter is used to extract part of the placenta inside the mother. Ultra sound and fetoscopy
are visual tests that are used.
Chapter 15 Chromosomes and Heredity – Objectives:
1) How do segregation, crossing over, and independent assortment lead to different genes
ending up in different combinations in the offspring?
Crossing over occurs in Prophase of meiosis I and it leads to the mixing of alleles on
homologous chromosomes. Independent assortment occurs due to there being multiple ways
of aligning different sets of chromosomes along the metaphase plate during Meiosis I and II
– leading to a mixing of traits inherited on separate chromosomes. Random fertilization
causes the union of any sperm with any egg that may e produced leading to more variation.
They introduce variations by mixing and matching – more details in powerpoint (important
question).
2) How did Thomas Hunt Morgan show that traits/genes are carried on chromosomes using
Drosophila? Show the Punnett squares for the F1 and F2 generations. (website 1)
Morgan showed that genes are carried on chromosomes because there was a three to one
ratio but all the white eyes were on the males, which shows that the eye color trait is carried
on the X chromosome.
P1
F1
XR
XR
XR
Xr
Xr
XR
XRXr XRXr
XRXR XRXr
XR Y XRY
XRY
XrY
Y
Y
3) What else did Morgan’s fruit fly experiment suggest other than the fact that
chromosomes carry genes?
Not only was this gene on a chromosome, but more specifically it’s on the X sex
chromosome, which disagrees with Mendelian Genetics.
4) What are some common characteristics of X linked traits?
When the gene is recessive, the “disease” always shows up in the males. Also, women
need two recessive to have it appear in them, and only one makes them a carrier.
Ms. Sastry
AP Biology
Leigh High School
5) What are linked genes? How are they inherited? (website 2)
Linked genes are non-Mendelian and are genes that are inherited together because the
whole chromosome is passed on as a unit. They are inherited through meiosis and gamete
formation when there is no crossing over to separate these genes – so all genes that are linke
will be passed on from one parent only.
6) What are recombinants? How do they arise? (website 3)
Recombinants are genes that cross over and are passed on. This occurs in meiosis I.
7) Show the parental and recombinant phenotypes in a comparison of meiosis end products
from linked and unlinked genes (website 2- last image):
8) If there is a <50% frequency of recombinant offspring in a test cross involving one
heterozygote, then the genes are said to be – linked.
9) What is recombination frequency – how can it be calculated? What is used to predict?
Recombination frequency can be used to estimate the distance between two genes. It can
be calculated by dividing the number of recombinants by the total number of offspring, then
multiply it by 100 to get the percent.
10) What are linkage maps? What is one map unit? Are they a true indication of actual map
distances?
Linkage maps are the relative position of genes along the chromosomes. One map unit
(centimorgan) is equivalent to a 1% recombination frequency. They just measure the distance
between two genes, not actual map distances.
11) What is the human genome project?
This is the project that was used for discovering and ‘ordering’ all of the genes within a
single human being.
12) How is sex (gender) determined in Drosophila and in humans?
In Drosophilia, the ratio of autosomes to X chromosome determines sex. Females are
with a ratio of 1:1 or more, while males are anything with a less than 1:1 ratio. In humans, a
Y is male and any number of X’s without a Y is female.
13) What is the SRY region?
This is the sex-determining region of the Y chromosome.
14) What are Barr bodies – where do they come from?
Ms. Sastry
AP Biology
Leigh High School
Barr bodies are the inactive extra X chromosome in females, which only become active
in the ova cells.
15) What are chromosomal aberrations?
These are alterations in chromosome structure or number and deviations from
chromosome theories of inheritance.
16) What is nondisjunction? Draw a sketch of how a Down’s syndrome offspring ends up
with 3 copies of Chromosome 21 (trisomy). Show the egg and sperm meiosis process in
the parents. (website 4)
Nondisjunction is when a chromosome doesn’t break into its sister chromatids or the
homologous chromosomes do not break apart in meiosis.
17) What happens to most of the disorders in chromosome numbers at an early stage of fetus
development?
Usually when a chromosomal problem is found in the early stages of a fetus, the body
terminates it from continuing on in growth.
18) What happens in Turner’s syndrome and Klinefelter’s Syndrome – explain what
aneuploidy means
Turner’s syndrome is when a girl’s sex chromosome genotype is XO. Klinefelter’s is the
opposite where the genotype is XXY, so the baby is a boy-girl. This results from
nondisjunction in meiosis. Aneuploidy means “abnormal number”, as in the wrong number
of chromosomes.
19) Explain what polyploidy means and what organisms are often polyploids?
Having more than two complete sets of chromosomes is called polyploidy. Plants usually
have this characteristic.
20) Describe what happens during translocation, duplication, and inversion of
chromosomes?
Translocation is when two unequal and non-homologous chromosomes switch parts of
their genes. Duplication is when a series of genes double them and put them back into the
gene sequence in the chromosome. Inversion is when a section of genes in a chromosome
flips upside down in the gene sequence.
Good animations:
1) Thomas Hunt Morgan's experiment with fruit flies
2) Linked Genes and Crossover Comparison between Unlinked Genes
3) Shows Crossing over In Regular and XY chromosomes
4) Down's Syndrome Nondisjunction Powerpoint and Animation
Ms. Sastry
AP Biology
Leigh High School
Chapter 16 DNA and its Replication – Objectives
1) How did the following scientists show that DNA and NOT protein is the genetic material
of the cell:
a) Griffith - Transformation- a change in genotype and phenotype due to the assimilation of a
foreign substance (now known to be DNA) by a cell. He studied Streptococcus pneumoniae, a
bacterium that causes pneumonia in mammals. One strain, the R strain, was harmless. The other
strain, the S strain, was pathogenic. In an experiment Griffith mixed heat-killed S strain with live
R strain bacteria and injected this into a mouse. The mouse died and he recovered the pathogenic
S strain from the mouse’s blood. This means that something (DNA) moved from the heat killed
S strain to the harmless R strain changing it to become pathogenic.
b) Avery - discovers DNA as the transforming substance (1944) by isolating various
macromoleculesin the heat killed S strain and mixing these individual parts with the R strain to
see which macromolecule caused the pathogenetic switch. In part, this reflected a belief that the
genes of bacteria could not be similar in composition and function to those of more complex
organisms.
c) Hershey and Chase - Further evidence that DNA was the genetic material was derived from
studies that tracked the infection of bacteria by viruses. Viruses consist of a DNA (sometimes
RNA) enclosed by a protective coat of protein. To replicate, a virus infects a host cell and takes
over the cell’s metabolic machinery. Viruses that specifically attack bacteria are called
bacteriophages or just phages. Used the radioactively labeled P32 (labels DNA) or S35 (labels
proteins) to figure out which part of the virus entered the bacteria – the DNA or the protein coat.
2) What is transformation?
A change in genotype and phenotype due to the assimilation of a foreign substance (now known
to be DNA) by a cell.
3) What is a bacteriophage?
Virus that infects bacteria
4) What was known to scientists before Watson and Crick worked on their model for DNA
structure? Also, what was unknown?
 DNA is polymer made of Nucleotides
 Nucleotides have sugar-phosphate-and a nitrogen base
 Nitrogen bases can be Adenine, Guanine, Cytosine, or Thymine
 Not known - how the monomers connect to make a molecule that can carry genetic
material
5) What did Chargaff observe and why was it critical to the discovery of DNA’s structure?
 DNA composition varies in different species
 In any one species, all 4 bases are not equal in number
 # of A = # of T (A=T)
 # of G = # of C (G = C)
6) What did Rosalind Franklin observe and why was it critical to the discovery of DNA’s
structure?
She took X ray crystallography picture of the DNA Structure. It allowed Watson and
Crick to correctly predict the structure of DNA as a double helix with the bases on the
inside.
7) Describe the Watson and Crick DNA model and draw a sketch of it. (- how are the sugar
and phosphates connected, where are the bases, how do they connect, what is the 3D
Ms. Sastry
AP Biology
Leigh High School
structure that DNA assumes … ). Use this website and click on Animation for an
excellent review of DNA structure discovery.
(http://www.dnaftb.org/dnaftb/19/concept/index.html)
The key breakthrough came when Watson put the sugar-phosphate chain on the outside and the
nitrogen bases on the inside of the double helix. The sugar-phosphate chains of each strand are
like the side ropes of a rope ladder. Pairs of nitrogen bases, one from each strand, form rungs.
The ladder forms a twist every ten bases. The nitrogenous bases are paired in specific
combinations: adenine with thymine and guanine with cytosine.
8) How does DNA replicate – conservatively, semiconservatively, or in a dispersive
fashion? Draw quick sketch to illustrate your answer.
Semiconservative
Ms. Sastry
AP Biology
Leigh High School
9) How did Meselson and Stahl prove the above using heavy isotope of Nitrogen?
(http://www.sumanasinc.com/webcontent/anisamples/majorsbiology/meselson.html)
Experiments in the late 1950s by Matthew Meselson and Franklin Stahl supported the
semiconservative model, proposed by Watson and Crick, over the other two models. In their
experiments, they labeled the nucleotides of the old strands with a heavy isotope of nitrogen
(15N) while any new nucleotides would be indicated by a lighter isotope (14N). Replicated
strands could be separated by density in a centrifuge. Each model: the semi-conservative model,
the conservative model, and the dispersive model, made specific predictions on the density of
replicated DNA strands.
•The first replication in the 14N medium produced a band of hybrid (15N-14N) DNA,
eliminating the conservative model.
•A second replication produced both light and hybrid DNA, eliminating the dispersive model and
supporting the semiconservative model.
10) Use the following animation and desribe how DNA replication occurs on the leading and
lagging strand in bullett form using our own words.
(http://www3.interscience.wiley.com:8100/legacy/college/boyer/0471661791/animations/
replication/replication.swf) Include the roles of helicase, primase, DNA polymerase,
DNA ligase, leading and lagging strands, continuous and discontinuous replication,
Okazaki fragments, replication fork, and ori sites.
 Replication begins at a specific site in the DNA called the origin of replication.
Unwinding enzymes called DNA helicases cause the two parent DNA strands to unwind
and separate from one another in both directions at this site to form two "Y"-shaped
replication forks. These replication forks are the actual site of DNA copying. During
replication within the fork, helix destabilizing proteins (not shown here) bind to the
single-stranded regions preventing the strands from rejoining.
 DNA polymerases can only add nucleotides to the free 3’ end of a growing DNA strand.
This creates a problem at the replication fork because one parental strand is oriented 3’>5’ into the fork, while the other antiparallel parental strand is oriented 5’->3’ into the
fork. At the replication fork, one parental strand (3’-> 5’ into the fork), the leading strand,
can be used by polymerases as a template for a continuous complimentary strand. The
other parental strand (5’->3’ into the fork), the lagging strand, is copied away from the
fork in short segments (Okazaki fragments). Okazaki fragments, each about 100-200
nucleotides, are joined by DNA ligase to form the sugar-phosphate backbone of a single
DNA strand.
 DNA Polymerase adds nucleotides
 As each nucleotide is added, the last two phosphate groups are hydrolyzed to form
pyrophosphate. The exergonic hydrolysis of pyrophosphate to two inorganic phosphate
molecules drives the polymerization of the nucleotide to the new strand.
 To start a chain requires a primer
 DNA Ligase joins the strands together
11) How does DNA proofreading and repair occur when a mistake has been made in the
replication process?
DNA polymerase proofreads each new nucleotide. If there is an incorrect pairing, the enzyme
removes the wrong nucleotide and then resumes synthesis.
Ms. Sastry
AP Biology
Leigh High School
12) What are telomeres and why could they represent the fountain of youth or be a cause for
cancer?
Telomeres are tandem DNA repeating sequences found at the end of chromosomes that
prevent chromosome degradation with every successive round of replication. If the
telomeres would not degrade after each division, then the human would be able to live longer
perhaps. Using this technique, telomerase – the enzyme that makes telomeres could be
injected and the cells could live longer. However, this could lead to cancer and mutations.
(http://www.wiley.com/legacy/college/boyer/0470003790/cutting_edge/telomeres/telome
res.htm)
Ms. Sastry
AP Biology
Leigh High School
Ms. Sastry
AP Biology
Leigh High School
Protein Synthesis Players and their Roles:
Players/Process
1) DNA - gene
2) TRANSCRIPTION
a) Promotor
b) RNA Polymerase
c) Transcription
Factors
d) mRNA
3) RNA PROCESSING
a) 5’cap and polyA tail
b) Intron
Prokaryote/
Eukaryote
Location of
player/process and
Structure
Function
What will
happen if
this player
fails/is
blocked?
Ms. Sastry
c) Exon
d) Spliceosome
e) Alternate Splicing
4) TRANSLATION
a) Ribosomes
b) Codon
c) tRNA
d) Anticodon
e) tRNA synthetase
f) Peptide bond
formation
AP Biology
Leigh High School
Ms. Sastry
AP Biology
Leigh High School
Ms. Sastry
AP Biology
Leigh High School
The Secret of Life
Monday, Jul. 14, 1958 Time Magazine
A few sprouted hopefully but did not grow. These were the
interesting spores. They acted as if they were trying to
grow, but needed something that they could not get from the
agar or produce for themselves. So when a microscope showed
such a spore, it was tenderly fed with vitamins, amino
acids and other growth-fostering chemicals in hope of
making it perk up and grow normally.
At the start of the experiment, Beadle and Tatum resolved
to make at least 1,000 tries before giving up. Such
perseverence was not necessary. On the 299th try they found
an ailing spore that needed only vitamin B-6 (pyridoxine)
to make it grow lustily. When it had mated with a normal
mold, it transmitted its need for vitamin B-6 to its
descendants in the proper Mendelian manner for a single
mutated gene.
This was what Beadle had been hoping for. His explanation
is that the gene damaged by X-ray violence was originally
responsible for producing an enzyme (organic catalyst)
needed in the mold's process of making vitamin B-6 out of
simpler nutrients. With the gene out of action, the process
stopped, and the mold could not grow without help. It was
like a human diabetic who needs an external source of the
insulin that his body cannot make.
New Attitude. When Beadle and Tatum reported their success
in 1941, they had quite a collection of defective molds,
each needing some extra nutrient or having some other genecontrolled chemical ailment. In a few years their imitators
filled their own laboratories with molds as unnatural as
the most monstrous fruit flies. The coral fluffs of normal
Neurospora are rare in the test tubes and Petri dishes. In
their place are blackish warts, lichenlike incrustations,
or sick-looking globules. One horrible kind of mold grown
in a moving liquid floats in bunches with limp limbs like
soft, dead crabs.
An immediate, practical result of Neurospora genetics was
the application of mold irradiation to wartime penicillin
production. Much more important were the long-range
Ms. Sastry
AP Biology
Leigh High School
scientific results. The success with Neurospora yielded new
techniques for using molds and other small organisms as
genetic tools. Out of its use flowed a new attitude toward
genetics. No longer were genes considered abstract units of
heredity. They became actual things, not entirely
understood but known to be concerned with definite chemical
actions. Professor Joshua Lederberg, 33, of the University
of Wisconsin, probably the world's leading young
geneticist, says that the Neurospora work at Stanford
clinched the whole idea that genes control enzymes, and
enzymes control the chemistry of life.
In 1946 Caltech needed a new head for its now famous
Division of Biology. Professor Morgan had retired. Beadle
was tapped for the job and accepted, knowing well that he
would have to curtail, perhaps abandon, his personal
research. Some of his friends felt that a great scientist
was being wasted on a routine administrative job, and there
was a precedent for their fears in the history of genetics.
Mendel himself did nothing of note after he was made abbot.
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AP Biology
Leigh High School
Sci Am News
June 13, 2007
The 1 Percent Genome Solution
The first results from a massive project to exhaustively
catalogue all the functions of the human genome reveal a
hotbed of activity in the gaps between genes. An
international consortium of researchers sifted through 1
percent of the genome looking for pieces of DNA that are
copied by the cell or help to control gene activity. The
results indicate that most DNA is copied into molecules of
RNA, including the long stretches between genes, and that
genes overlap and interact with each other much more than
researchers previously believed.
"We all suspected there was interesting stuff going on in
these regions [between genes], and sure enough there is,"
says bioinformatician Ewan Birney of the European
Bioinformatics Institute near Cambridge, England, a member
of the project's computer analysis team.
Although researchers do not yet know the biological
significance of these discoveries, they say that fully
cataloguing the genome may help them understand how genetic
variations affect the risk of contracting diseases such as
cancer as well as how humans grow from a single-celled
embryo into an adult. The next phase of the project, set to
begin later this year, will attempt to inventory the full
genome.
A genome consists of only four different nucleotide bases,
or DNA subunits, arranged in a particular sequence. The
publication of the human genome in 2001 revealed its
sequence—the significance of which remains a mystery. In
particular, genes account for only 1.2 percent of the
genome's three billion bases. Once dismissed as "junk DNA,"
researchers have found that some of these so-called
noncoding regions are shared among mammals, suggesting they
play an important function.
To help uncover those functions and identify other
important sequences, 35 research groups joined forces in
2003 to create the encyclopedia of DNA elements (ENCODE)
project. This consortium selected 44 separate sections of
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AP Biology
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the genome that included regions of high to low gene
density and high to low similarity between mouse and human.
Like treasure hunters combing a vast beach with metal
detectors, ENCODE researchers sifted through their patch of
the genome in multiple ways that are described, along with
the results, in a Nature paper published online today and
in a special issue of Genome Research.
A major part of the project was identifying sequences that
cells copy, or transcribe, into RNA molecules. Cells make
proteins from RNA they copy from genes, but some RNAs play
roles by themselves. In addition, some studies have found
evidence that species from flies and worms to humans copy
large amounts of RNA from noncoding DNA, with no apparent
purpose. Nevertheless, "before ENCODE, I think a lot of
people were skeptical of how real intergenic activity was,"
says bioinformatician and consortium member Mark Gerstein
of Yale University.
Although genes make up only 3 percent of the ENCODE
sequence, the consortium found that 93 percent of the
sequence is transcribed. Some of the transcripts hail from
noncoding DNA, the researchers report, but those that do
match up with the 399 ENCODE genes overlap with each other
extensively.
Transcripts from 65 percent of the genes incorporate pieces
of DNA from relatively far outside of the genes or even
from one or two other genes, says molecular biologist and
consortium member Tom Gingeras of Affymetrix, a genome
technology company in Santa Clara, Calif. Researchers know
that cells chop single genes into shorter pieces called
exons, which they mix and match into one transcript for
creating a protein. Gingeras says the ENCODE findings
confirm recent reports that humans and flies sometimes
combine exons from two different genes.
Based on the transcript sequences, the researchers
identified 1,437 new promoters—short DNA sequences where
transcription begins—in or between genes, on top of the
1,730 promoters they knew of. That is nearly ten promoters
per gene, Birney says. He adds that the abundance of
transcripts that overlap each gene suggests that the very
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AP Biology
Leigh High School
term "gene" should mean something different inside the cell
nucleus, where transcription takes place, than outside of
it, where finished proteins go.
Project members also catalogued sequences that mark areas
where DNA unwinds from the round histone proteins that
maintain the shape of chromosomes, allowing the cell's
transcription machinery to activate genes in those areas.
They discovered some potentially unwound areas that are far
from promoters and may therefore play some other role,
Birney says.
The consortium found that 5 percent of the studied sequence
has been conserved among 23 mammals, suggesting that it
plays an important enough role for evolution to preserve
while species have evolved. But of all the new ENCODE
sequences identified as potentially important, only half
fall into the conserved group.
These unconserved sequences may be "bystanders," Birney
says—consequences of the genome's other functions—that
neither help nor hurt cells and may have provided fodder
for past evolution.
They could also simply maintain a useful DNA structure or
spacing between pieces of DNA regardless of their
particular sequence, says genomics researcher T. Ryan
Gregory of the University of Guelph in Ontario, who was not
part of the consortium.
"The biological insights are mainly incremental at this
point," says genome biologist George Weinstock of the
Baylor College of Medicine in Houston, which he says is to
be expected of such a pilot study. "This is a 'community
resource' project, like a genome project, that makes lots
of new data available to the community, who then dig into
it and mine it for discoveries."
Gregory says the results, although still cryptic, do hint
at new functions and a more complicated genome. "This study
shows us how far we are from a comprehensive understanding
of the human genome."