Ch 14.2, 14.3, 14.5, 14.6

DNA polymerase is used to

"read" the template strand. "read" the template strand. Incorrect synthesize the daughter strand. cut the daughter strand.

Initiation of DNA replication

- DNA is unwound at origin of replication by helicases producing two replication forks on either side

Lagging strand synthesis

- Discontinuous synthesis • DNA pol III - RNA primer made by primase for each Okazaki fragment - All RNA primers removed and replaced by DNA • DNA pol I - Backbone sealed • DNA ligase •Termination occurs at specific site - DNA gyrase unlinks 2 copies

A can form ____ H-bonds with T

2

X-ray diffraction was used to determine that the diameter of a DNA molecule is

2 nm

G can form _____ H-bonds with C

3

components of DNA

5 carbon sugar, phosphate group, nitrogenous base

ribose sugars found in nucleic acids consists of

5 memebred ring four carbon atoms oxygen atom

A segment of DNA has the sequence 5'-ATGCCC-3'. The complementary sequence would be

5'-GGGCAT-3'

replication fork

A Y-shaped region on a replicating DNA molecule where new strands are growing.

lagging strand

A discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each synthesized in a 5' to 3' direction away from the replication fork.

Telomerase uses which of the following as a template?

A short internal RNA

What is a thymine dimer?

A site where two adjacent thymine bases become covalently cross-linked to each other

DNA gyrase

A topoisomerase which adds negative supercoils to the template DNA during the replication process. This process a) removes the positive supercoils caused by helicase and b) promotes strand separation.

helicase

An enzyme that untwists the double helix of DNA at the replication forks. requires ATP

endonucleases

Cut DNA backbone in a strand of DNA; facilitate repair and insertions (internally)

Replicons

DNA controlled by an origin individual units of replication

lab info

DNA exists in all cells but is housed inside the nucleus of eukaryotic cells. In order to extract it, associated proteins and membranes must be removed. DNA is released by cell lysis in a sodium chloride solution that makes the DNA more readily condense when later exposed to alcohol. Detergent in the solution emulsifies membrane lipids and proteins, keeping them from interacting with DNA. Protein-digesting enzymes in meat tenderizer degrade proteins, which then releases the DNA. Cold ethanol causes DNA to precipitate (solidify and become visible) while preserving fragile hydrogen bonds, thus preventing damage to the strands. DNA isolation is an important procedure that allows researchers to study how DNA functions. Keeping all reagents cold in this simulation protects the DNA from breakage.

Explain why DNA polymerase can only add nucleotides in a 5' to 3' direction. What implication does this have on the telomeres of the lagging strand?

DNA polymerase can only add nucleotides in one direction. It adds to the 3' end of the template. The reason for this is because the OH group is found at the 3' end. The OH group serves to carry out a nucleophilic attack on the phosphate group that has a complementary base. On the lagging strand, there is no place for a primer to be made so the DNA fragment is copied at the end of the chromosome. This can be a problem because the cell isn't able to repair and if it continues the ends keep getting shorter when the cell divides. Along with this telomeres keep getting shorter also during DNA replication. But the enzyme telomerase sticks to the end of the DNA strands allowing the complementary bases of the RNA template to add to the DNA strand which then allows DNA polymerase to keep adding nucleotides

Which of the following facilitates the reversal of damage to our hereditary material before a permanent mutation can occur?

DNA repair systems

Termination of DNA replication

During termination, primers are removed and replaced with new DNA nucleotides and the backbone is sealed by DNA ligase.

Why is DNA replication called semi-conservative?

Each daughter DNA molecule is composed of one parental strand and one new strand.

Dispersive model of DNA replication

Each strand of both daughter molecules contain a mixture of old and newly synthesized DNA

The model organism used by Meselson and Stahl was

Escherichia coli.

Which types of cells have more than one origin of replication?

Eukaryotes

In order for mismatch repair to occur in a bacterial cell, the enzyme machinery must be able to distinguish between the template strand and a newly synthesized strand. How is that achieved?

For a short period of time after replication, the sequence GATC is methylated at the A only on the template strand.

Prevent supercoiling upstream of the replication fork

Gyrase

Unzips (separates) DNA strands

Helicase

Discuss why each of the following components were used in the DNA extraction activity. Be specific (for example, if you tell me it breaks down protein, tell me what protein and why this is important) Ice Sodium Chloride Detergent (soap) Meat tenderizer 95% ethanol

Ice : The ice was important as it was used to keep the filtrates and reagents cold. The cold temperature stabilizes DNA preventing it from breakage. Sodium Chloride : The sodium chloride was used as the sodium ions neutralize the negative charge of the DNA. When the negative charge is neutralized it allows for precipitation to occur which helps the DNA come out of the solution. Detergent (soap) : The detergent/soap helps emulsify the cell as well as the nuclear membranes of the cell. This is due to the disruption of phospholipid bilayers. One the membranes are pulled apart the DNA is released from the cell. Meat tenderizer : The meat tenderizer was used to digest associated proteins that bind the DNA. It is important that the proteins must be removed because they help organize DNA into packed structures within cells. This allows the DNA to be more accessible. 95% ethanol : The 95% ethanol was used to precipitate the DNA from filtrate. DNA precipitates when it enters the ethanol because it is not soluble in ethanol but it is in the water based filtrate. Once the DNA has precipitated it becomes available to be spooled. the meat is able to digest those proteins thanks to enzymes found in meat which allows DNA to be released. The cold ethanol helps preserve H-bonds which helps with preventing the damage to strands.

If a DNA sample contains 13% adenine, what percentage of the sample contains cytosine?

If a DNA sample contains 13% adenine, what percentage of the sample contains cytosine?

Tautomers

Isomers that can interconvert by exchanging the location of a proton.

sequence resulting from a replication of the DNA sequence

It is involved in assembly of the daughter strand using the parental strand as a template.

On this strand, the removal of the last primer leaves a gap that cannot be primed at the ends of the chromosome.

Lagging

Compare and contrast the leading strand and lagging strand in the context of DNA replication

Leading Strand - During DNA multiplication, replicataes - Does not require DNA ligase for growth -Drirection of growth is 5' to 3' -Single RNA primer required - Formation is quite rapid Lagging strand -During DNA replication, replicates in fragments called Okazaki fragment and its growth is discontinuous -DNA ligase required for joining Okazaki fragments -fDirection of growth is 3' to 5' although each odazaki fragemtn is 5' to 3' - in each new okazaki fragment new RNA is required -formation is slower lagging strand is replicated in okazaki fragments and is discontinuous. This is due to the single stranded binding proteins primase and DNA polymerase being short lived. The template strand would be degraded if they waited for the entire strand to get unzipped and start copying the strand of DNA. Therefore as helicase begins to unzip a section of the DNA primase and DNA polymerase immediately begin to work on that section.

Seals up the two new DNA strands

Ligase

_________repair is responsible for removing bases that were incorrectly incorporated into DNA during replication.

Mismatch

What type of repair mechanisms is responsible for removing bases that were incorrectly inserted into DNA during replication?

Mismatch repair

What is the name of the subunit that acts as the sliding clamp, which keeps the replicating enzyme complex attached to the template in eukaryotic cells.

PCNA

Creates new strands of DNA by adding complementary nucleotides

Polymerase

Identifies the replication start locations by adding RNA primers

Primase

Which of the following enzymes involved in DNA replication are found at the replication fork in all three types of cells (bacterial, archaeal, and eukaryotic)? Choose all that apply.

Primase Helicase Polymerases Sliding clamp Clamp loader

Elongation of DNA replication

Proteins connect the correct sequences of nucleotides into a continuous new strand of DNA

supercoiling

Repeatedly coiling DNA molecule to make chromosome shorter and wider.

leading strand synthesis

Single priming event Strand extended by DNA pol III

Okazaki fragments

Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.

Consider a double stranded DNA molecule. In complementary base pairing, A pairs with _________and C pairs with________

T or thymine G or guanine

What is the name of the regions at the ends of eukaryotic chromosomes?

Telomeres

Which of the following are short repeats of DNA on the ends of eukaryotic chromosomes?

Telomeres

Explain the complimentary base pairing rules of DNA. Why does A always go with T and C always goes with G.

The complimentary base pairing rule is Charagaff's rule and it states that DNA base pairs are always adenine with thymine and cytosine with guanine. The reason for this is because Charagaff discovered that in any DNA molecule, the percentage of guanine is always approximately equal to the the percentage of cytosine and the same goes with adenine and thymine. Another reason is A and T are connected by two hydrogen bonds and C and G are connected by three hydrogen bonds. I agree the H-bonds shared between A with T and C with G allow their bonds to be stronger and more stable. A and G are purine bases that have two rings while T and C have a single ring. Bonding of A and G bonded would take up too much space between the strands.

leading strand

The new continuous complementary DNA strand synthesized along the template strand in the mandatory 5' to 3' direction.

Explain what is meant by the description: "DNA strands are antiparallel"

The reason the strands are described as antiparallel is because one strand is oriented on the 5'to3' while the other one is on the 3' to 5' direction which allows the strands to connect to each other

In the DNA isolation process, how was the DNA stabilized?

The test tube was placed in an ice bath.

Why do eukaryotic cells have multiple origins of replication?

To ensure timely replication of multiple, relatively large chromosomes

semiconservative model

Type of DNA replication in which the replicated double helix consists of one old strand, derived from the old molecule, and one newly made strand.

replisome

a complex of DNA polymerase and other enzymes that catalyze the synthesis of DNA proteins has two subcompartments the primosome and a complex of two DNA pol III enzymes on for each strand

Features of the Watson and Crick model include

a sugar phosphate backbone a double stranded structure a helical structure

The DNA structure proposed by Watson and Crick involves

a sugar phosphate backbone two grooves (major and minor) a helical structure

DNA polymerase I

acts on the lagging strand to remove primers and replace them with DNA

In DNA replication, _______________________ pairs with thymine, and cytosine pairs with _______________________.

adenine; guanine

exonuclease

an enzyme that removes successive nucleotides from the end of a polynucleotide molecule

DNA's phosphodiester_________- is composed of sugars and phosphates.

backbone

Nucleotides contain a sugar, a phosphate, and a nitrogenous_______

base

Telomeres are related to

cellular aging

models of DNA replication

conservative, semiconservative, dispersive

primosome

consistis of primase and helicase along with a number of accessory proteins

Franklin used x-ray________ to suggest that DNA has a helical structure. Listen to the complete question

diffraction or crystallography

In order for mismatch repair to occur in a bacterial cell, the enzyme machinery must be able to

distinguish between the template strand and a newly synthesized strand.

DNA polymerase II

does not play a role in replication but is involved in DNA repair process

The interaction of two strands of DNA via hydrogen bonds is the

double helix

The level of DNA structure that resembles a spiral staircase is the

double helix

List the three phases of DNA replication:

elongation initiation termination

In the DNA isolation process, detergent was used to

emulsify cellular and nuclear membranes.

DNA primase

enzyme that is a RNA polymerase that synthesizes short stretches of RNA 10 to 20 base pairs long that function as primers for DNA polymerase. Later on the RNA primer is removed and replaces with DNA

DNA polymerase

enzyme that matches the existing DNA bases with complementary nucleotides and then links the nucleotides together to make a new strand

topoisomerases

enzymes that change DNA supercoiling an enzyme that can alter the topological state of DNA relieve the torsional strain

The two main eukaryotic DNA polymerases that extend DNA are

epsilon delta

the amount of adenine present in DNA always ____ the amount of thymine and the amount of guanine always ____the amount of cytosine

equals

Based on replication proteins, DNA replication in archaea is most similar to that of

eukaryotes

This type of primase is a combination of RNA polymerase and DNA polymerase that makes short RNA primers and then extends them with DNA to produce the final primer:

eukaryotic

Removes RNA primers

exonuclease

The primary purpose of the Meselson and Stahl experiments was to determine

how DNA replicates.

The two strands of nucleotides in a DNA molecule are held together by

hydrogen bonds between nitrogenous bases.

Ethanol is used in the DNA isolation process because

it allows the precipitate to form.

double helix strands are made up of

king polymers of nucleotides each strand is made up of repeating sugar and phosphate units joined by phosphodiester bonds. it is known as the phosphodiester backbone of the molecule

DNA replication in eukaryotic cells is complicated by the fact that eukaryotic cells have

linear chromosomes

In an aging cell, the activity of telomerase would be

low

DNA polymerase III

main replication enzyme it is responsible for the bulk of DNA synthesis

In the DNA isolation process, ________ is used to break down the protein complexes and allow the DNA molecules to easily precipitate.

meat tenderizer Correct

Replicons in Eukaryotes

multiple origins of replication for each chromosome

Agents that cause mutation are known as

mutagens

Radiation, UV light, x-rays, and chemicals in the environment can cause mutations in DNA and are therefore referred to as

mutagens

Select all of the following that are components of a nucleotide.

nitrogenous base phosphate group sugar

When using a ladder analogy to describe DNA structure, the rungs of the ladder are composed of

nitrogenous bases.

DNA is a polymer. The monomers that make up this polymer are

nucleotides

The monomers that make up DNA molecules are called

nucleotides

Of the following list, which 3 items are required for DNA replication

nucleotides polymerase template

Where would the majority of the DNA be located within a eukaryotic cell?

nucleus

List several differences in prokaryotic and eukaryotic replication.

number of origins of replication complexity of enzymology structure of chromosome (linear vs. circular)

During semiconservative DNA replication

one of the strands in each new double helix comes from the original molecule, and one is newly synthesized.

Conservative model of DNA replication

parental double helix remains intact, both strands of daughter helices are newly synthesized

The main components of the a DNA nucleotide are (choose all that apply):

phosphate deoxyribose Nitrogenous base

phosphodiester bond

phosphate group is linked to the two sugars by means of ester bonds.

The DNA backbone is composed of

phosphate groups. sugars.

The backbone of DNA is made up of nucleotides that are held together by

phosphodiester bonds

Damage caused by UV light leading to thymine dimers is corrected during photorepair by the enzyme ______.

photolyase

The function of telomeres is to

protect the ends of chromosomes

DNA polymerase I,II and III

removes the RNA primer and replaces it with DNA they all synthesize polynucleotide strands only in th e5'-3' direction and require a primer

DNA replication is considered to be

semiconservative

the basic mechanism of DNA replication is

semiconservative

DNA replication that leads to the production of double helices with one parental strand and one newly synthesized strand is consistent with

semiconservative replication

prokaryotic replication starts at _______ point(s) and it ends at a specific site called the _______

single origin (oriC) terminus

______-repair systems target a single kind of lesion in DNA and repair only that damage, while ________repair systems use a single mechanism to repair multiple kinds of lesions in DNA.

specific nonspecific

discovered DNA

swiss chemist Friedrich miescher

The enzyme______ contains a small internal piece of RNA, which is used as a template to extend the end of a linear DNA molecule.

telomerase

Short, repeated sequences of DNA are characteristic of

telomeres

DNA replication requires

template (parental DNA) nucleotides (building blocks) polymerase enzyme ((preform actions of copying the template)

What is DNA isolation?

the extraction of DNA from viruses or cells

Eukaryotic replication complicated by two main factors

the larger amount of DNA organized into multiple chromosomes and the linear structure of the chromosomes

The problems in replicating the ends of linear chromosomes are caused by (choose all that apply)

the need for a primer the directionality of polymerases

DNA repair mechanisms have likely evolved because

there is no way for cells to avoid exposure to mutagens