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1) Why are gyrase and helicase required for replication?




Both are used to aid in unwinding of DNA for replication

Gyrase (an enzyme) reduces the torsional strain that builds up ahead of
the replication fork as a result of unwinding

STEPS OF REPLICATION OF DNA: 1) Gyrase separates & Helicase unwinds
 2) Polymerase add Nucleotides to each sides that are separated  3)
then pairing up with GC & AT occurs  4) Proofreading occurs via

Polymerase ( pairing up mistakes can either be repaired with replacement
of self-destruct if too many)  5) Ligase then comes in to seal up &


create long continuous strands  6) winds back up to new DNA now

In E
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In E
...


Enzyme reverse transcriptase uses RNA as a template, it makes a DNA
molecule
...


DNA primase synthesizes RNA primers using the single-strand DNA
templates
...


DNA synthesis during replication is initiated from RNA primers
...
The double helix model of DNA suggested
to Watson and Crick that DNA could be replicated by semiconservative

replication
...

3) What is the difference between primase and polymerase?
POLYMERASE FACTS:






All DNA polymerases synthesize new DNA by adding nucleotides to the 3’
OH of the growing DNA chain
...


DNA polymerases require template, primer, free 3 OH’, & dNTP’s for DNA
replication
...


DNA polymerases cannot synthesize a DNA from scratch without a
primer
...
The consequence of this

mutation will be that the DNA strands would contain pieces of RNA
...
coli:

They require a primer to initiate synthesis
...


They produce newly synthesized strands that are complementary and
antiparallel to the template strands

They synthesize in the 5′  3′ direction by adding nucleotides to a 3′-OH
group
...


DNA primase requires a DNA template and RNA nucleotides to initiate
primer synthesis
...


 Primase synthesizes primers in order to have Polymerase start up to work
 PRIMASE & POLYMERASE BOTH ENZYMES

4) What is a replication fork and how many are there for prokaryotic replication? How
many are there for eukaryotic replication?


The Replication Fork is the site or junction/section where double-stranded



Prokaryotes have only TWO



DNA splits apart into 2 single strands

Eukaryotes have MANY, creating bubbles where the parent strands are being
separated
...


DO: SSB plays a role in separating DNA strand during replication and prevent
ssDNA from re-form a double helix
...
K
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Leading Strand  synthesized continuously

At a replication fork, both strands are synthesized in a 5′ → 3′ direction
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Okazaki fragments has nicks and are sealed with DNA ligase
...
They are

complementary to the lagging template strand, together forming short doublestranded DNA sections
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9) Ribose sugars have a hydroxyl on the 2nd carbon
...
This is

because DNA lacks a free hydroxyl group on the 2′-carbon atom of its sugar
...
Describe the experiment
...
~ TRUE


Discovered: "the transforming principle" that could genetically alter
bacteria



Experiment: Frederick Griffith studied two strains of the bacterium

Streptococcus pneumoniae
...
Bacteria of
the R (rough) strain lack a capsule and are nonpathogenic
...


~ trying to develop a vaccine against pneumonia
...
What are the differences between DNA and
RNA? What are similarities?
Similarities:

(1) DNA and RNA contain purine and pyrimidine nitrogenous bases, one benzoic
acid radicle and one pentose
...

Differences:

(1) The RNA specific nitrogenous base is uracil while the specific DNA
nitrogenous base is thymine
...


12) True or false: There are three phosphates between each sugar in a molecule of
DNA
...
An enzyme called T-antigen (helicase) binds to the origin and
unwinds the DNA in both directions from the origin
...
**OH group

18) What are the steps for theta replication?



Circular DNAs, including bacterial chromosomes and plasmids
Either Unidirectional or Bidirectional

Two types of theta replication  could either be single replicon which is replication
of the entire chromosome initiated at a single site (oriC in E
...
Does it? ~ FALSE

20) In a transcription reaction, two phosphate groups are cleaved from the incoming
ribonucleoside triphosphate; the remaining phosphate group is attached to the
growing RNA molecule by a phosphodiester bond
...
What is one possible problem?
There is a mutation at –10, where a promoter consensus sequence is
located
...


Example: suppose that you have the DNA sequence from ten individuals:
ATAGGGCTAAAAT
ATTGGCCTAAAAT

ATAGGGCTAAAAT
ATCGGGCTAAAAT

ATAGGGCTAAAAA
ATAGGGCTAAAAT
ATTGGGCTAAAAT

ATTGGGCAAAAAT

ATAGGGCTAAAAG
ATAGGGCTAAAAT

* There are some differences, but at each position there is an obvious common

letter which makes the consensus sequence= ATAGGGCTAAAAT
23) Describe the mechanism of rho independent termination
...


(2) Rho-independent transcription termination relies on a hairpin in the
transcribed RNA that causes RNA polymerase to pause, facilitating
termination
...


(1) Rho-dependent transcription termination relies on a lack of RNA secondary

structure so that rho can bind the RNA, move up to the RNA polymerase, and
remove the RNA from the DNA template
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26) It is possible for a repressor to negatively regulate the expression of an
operon because:

A
...

B
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 C
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D
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27) What is the difference between a transcription regulation system that uses induction
and a system that uses repression?
Induction: Stimulates expression of a gene in response to a specific substrate
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~OR~

Induction: Transcription is normally off and is stimulated in response to a
specific substrate
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 Operons are a form of transcriptional control
...


30) How can you access DNA to transcribe a gene? How can you modify or move
around histones?



Different genes may be transcribed from different strands of DNA

Arginine in the amino acids has a positive charge that helps to hold the

DNA in contact with the histones


0 types of histones are found in the nucleosome that packages

mitochondrial DNA


The Histone Code consists of modifications to histone proteins that

affect the expression of DNA sequences
...



They performed experiments showing that DNA is the genetic material of



The Hershey-Chase experiment was a landmark study because it

a phage known as T2
...



EXPERIMENT: Alfred Hershey and Martha Chase used radioactive sulfur

and phosphorous to trace the fates of protein and DNA, respectively, of T2
phages that infected bacterial cells
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32) How is Hershey and Chase experiment similar to Fraenkel-Conrat and Singer’s?


Hershey-Chase experiment dealt with bacteria and found that DNA was the genetic

material




Singer’s experiment dealt with viruses and found that RNA was the genetic material

But they both worked with proteins as well

33) What are conformations of DNA?
34) How do telomeres protect themselves from endonuclease activity?

The repeated sequences at telomeres, work to protect chromosome by: 1) Serve
as binding sites for protective proteins & 2) Prevent chromosomes from fusing
35) How did Watson and Crick figure out the semi-conservative nature of DNA
replication? (Yes… it has to do with those heavy isotopes… and yes… you have to
know about it!)
Watson and Crick figured that this model would result in two new double

strands of DNA, each one with one strand of parent (or template) DNA and one
strand of daughter (or newly-synthesized) DNA
...


Meselson and Stahl decided the best way to tag the parent DNA would be to

change one of the atoms in the parent DNA molecule
...
So they decided to use an
isotope of nitrogen to distinguish between parent and newly-copied DNA
...

You can see from any periodic table that most nitrogen atoms have an atomic
weight of 14
...
But an isotope with an extra neutron
has a weight of 15, so we call it N-15
...
If only N-14 nucleotides were
available during DNA replication, they would be able to tell which parts had

come from the original double strand and which parts had been created during
the replication process
...
Is this a prokaryotic or eukaryotic system?
*REPLICATION ORIGIN:

Eukaryotes - Several ORiCs, therefore several replication bubbles

Prokaryotes - One ORiC, and since they have a single circular chromosome, the
replication bubble formed is going to make the entire thing look like the Greek
letter Theta (why it is called Theta Replication)
...


 Continuous DNA polymerization occurs for the leading strand while
discontinuous DNA polymerization occurs for the lagging strand
...


 DNA polymerase I “repairs” the RNA primers and replaces RNA with DNA
...


39) What does telomerase do?


SUMMARY



Telomerase activity is most likely to be found in germ line cells in humans




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Expressing telomerase in somatic cells causes cancer

Telomerase uses an RNA template to synthesize new DNA
HUGE EXPLANATION

Telomerase allows for the ends of chromosomes to be replicated
...
In order for the

chromosomes to be maintained for use in the next generation, telomerase


must be expressed in cells of the germ line
...
Because of this,

somatic cells normally can divide only a limited number of times before the

telomeres are completely removed and the chromosomes become unstable
...
Because the telomeres are restored after replication, these cells
are able to divide an unlimited number of times, allowing cancer cells to

reproduce themselves without limit and allowing tumors to grow to large
size and cancer to spread within the body
...
Aging occurs
because as cells continuously divide and the tips of the chromosomes

(telomeres) shrink over time
...


41) What are differences between constitutive and regulated gene expression?

A constitutive gene is a gene that is transcribed continually compared to a

facultative gene which is only transcribed when needed, while a Regulation of
gene expression (or gene regulation) includes the processes that cells and

viruses use to regulate the way that the information in genes is turned into
gene products
...
Euk?


Eukaryotes have the following:

(1) RNA polymerase I and it transcribes large rRNA
...


45) Describe initiation of Eukaryotic transcription – the Binding of RNA polymerases to
the promoter


Promoter is the sequence of DNA where transcription is initiated



Promoters are required for transcription along with Ribonucleotides, DNA






Promoters are usually located upstream of the start site
template, RNA polymerase

RNA polymerase binds to a promoter to initiate transcription
In eukaryotic transcription:

(1) Eukaryotic transcription involves a core promoter and a regulatory
promoter
...


(3) Chromatin remodeling is necessary before certain genes are
transcribed
...


The TATA-binding protein (TBP) binds to the TATA box sequence in

eukaryotic promoters its function in transcriptional initiation is to bend
and partly unwind DNA at a promoter
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Which syndrome shows evidence that some
type of transcription-specific DNA repair mechanism exists?




DNA polymerase I “repairs” the RNA primers and replaces RNA with DNA
...

More specifics below:

(1) DNA polymerase : initiation of nuclear DNA synthesis and DNA repair
(2) DNA polymerase : replication and repair of mitochondrial DNA

(3) Other eukaryotic DNA polymerases (and  allow DNA replication to

proceed past damaged regions of DNA (DNA lesions), or to play various
roles in DNA repair processes

47) Describe how Trp operon works
...
The trp
operon is present in many bacteria, but was first characterized in E
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

A strain of E
...
coli trp-

Additional Study Guide for CH
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6

Section 5
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1 - Interactions among the human ABO blood group alleles involve



Epistasis is when two or more loci work together to get a phenotypic



co-dominance and complete dominance
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EPISTATIC INTERACTIONS

Recessive epistasis = 9:3:4


Hair color is determined in Labrador retrievers by alleles at the B and E
loci
...
Alleles at a second locus affect the
deposition of the pigment in the shaft of the hair; dominant allele E

allows dark pigment (black or brown) to be deposited, whereas recessive
allele e prevents the deposition of dark pigment, causing the hair to be
yellow
...
Two pink panthers fall
in love and produce a large litter of baby panthers with the following

phenotypic ratios: 12/16 pink; 3/16 black; and 1/16 white
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In a cross between a black beetle
and a white beetle you obtain a ratio of 9 black to 7 white beetles
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A true-breeding

white mutant is mated with a different true-breeding white mutant
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When the purple F1 offspring mate with each other,

their offspring occur in the ratio of 9 purple: 7 white
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o EX
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3 - Sex-influenced and sex-limited traits

 Huntington disease tends to strike earlier and lead to a more rapid

progression of symptoms as it moves from generation to generation
...
Which genetic
phenomenon (or phenomena) is (are) likely operating here?

All of the following  Parental imprinting, Genetic anticipation, Sex-linked
inheritance, Incomplete penetrance

IMPRINTING = deleted or silenced, not affecting the DNA sequence



The phenomenon in which a gene’s expression is determined by its
parental origin is called genomic imprinting

Imprinting is when a gene is silenced because of either from mom or dad
o
o



Silencing genes happen through DNA methylation, methyl groups

acting as labels to know which genes to express and not to express
Heritable diseases can be due to deletion, mutations, incorrect
labeling, NOT JUST GENETICS

A deletion of a small region on the long arm of chromosome 15 causes a

developmental disorder in children called Prader-Willi syndrome when the
deletion is inherited from the father
...
What type of genetic phenomenon does this
represent? Genomic Imprinting

ANTICIPATION


What phenomenon describes a genetic trait that is expressed more

strongly or earlier in development with each generation? Anticipation

Chapter 6 – Pedigrees & Genetic Testing

PEDIGREES = showing phenotypes of families & family relationships

o Proband – first affected family member to seek medical attention
with a medical condition

Autosomal recessive traits = parents usually start unaffected but heterozygous
carries of a disease and pass it down to their children
1
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2
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3
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4
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 1 out of 4 kid gets it

 EX
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The other three

children are phenotypically normal
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 EX
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Two unaffected parents can have an affected child
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 EX
...


Affected females always have an affected father and an affected maternal
grandfather
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Autosomal dominant


Passing down from affected parent to their children
o Doesn’t matter if female or male

 EX
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Sex Linked conditions are more often males showing the disease more

X-linked recessive

 X-linked recessive trait in humans:

 An affected man often has phenotypically normal parents
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 An affected man usually has a mother who carries the recessive allele
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X-linked dominant

 Most pedigrees showing the hypothetical human trait show the following
characteristics is for X-linked dominant:
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
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Females are affected twice as frequently as males
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Half the children of affected mothers and normal fathers are affected
...


 Most pedigrees showing the hypothetical human trait show the following
characteristics for Y-linked:
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

Only males are affected
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Mitochondrial

 Several members of a family have a very rare form of hearing disorder
...
The most likely mode of inheritance is
mitochondrial since affected females pass the condition on to all their
children and affected males do not
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Twin studies

 Normally used to study the inheritance of human traits or disorders
Genetic influence

 EX
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Concordance rates of 30–50% have been found for Type
I diabetes with concordance rates of 80% for Type II
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What does this
information suggest concerning the relative effect of genetic and

environmental factors for each type of diabetes? Genetic influences exert a
larger role in Type II diabetes than in Type I diabetes
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1 - Imagine that a human characteristic is determined by genotype only,
with no environmental influence
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 EX
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How did you interpret
these data? (MZ = monozygotic twins and DZ = dizygotic twins
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Genetic testing


Preimplantation genetic testing involves testing a single cell of an early
embryo for a genetic disorder before the embryo is considered for
implanting into the mother’s uterus
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 The symptoms of some genetic conditions can be prevented by early
treatment
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 Parents who are considering children can determine if they are
heterozygous for a homozygous recessive condition
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 A woman who knows the genotype of the embryo or fetus she is

carrying may use the information to prepare for the birth of a child
with an inherited condition
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