CHAPTER 10 Flashcards by Miyaki Jan Lim

Naturally occurring DNA exists in single-stranded and double-stranded forms, both of which can exist in what forms

linear and circular forms

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most of the details we discuss were first investigated in prokaryotes, particularly

E. coli

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Mechanisms by which information is transferred in the cell is based on

Central Dogma

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Central Dogma

DNA replication
Transcription and reverse transcription
RNA transcription
RNA translation

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involves separation of the two original strands and synthesis of two new daughter strands using the original strands as templates

Replication

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what type of replication is where each daughter strand contains one template strand and one newly synthesized strand

Semiconservative replication

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explain the Meselson-Stahl experiment

Incorporation of isotopic label as sole nitrogen source (15NH4Cl)

Observed that 15N-DNA has a higher density than 14N-DNA, and the two can be separated by density-gradient ultracentrifugation

The experimental evidence for semiconservative replication. Heavy DNA labeled with 15N forms a band at the bottom of the tube, and light DNA with 14N forms a band at the top. DNA that forms a band at an intermediate position has one heavy strand and one light strand.

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was a series of experiments conducted in the 1950s that demonstrated how DNA replicates semi-conservatively.

Meselson-Stahl experiment

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DNA double helix unwinds at a specific point called an

origin of replication

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Polynucleotide chains are synthesized in both directions from the origin of replication; DNA replication _________, most organisms

bidirectional

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At each origin of replication, there are _____________, points at which new polynucleotide chains are formed

two replication forks

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There is one origin of replication and two replication forks in what type of DNA

circular DNA of prokaryotes

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In replication of a __________ chromosome, there are several origins of replication and two replication forks at each origin

eukaryotic

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The 3’-OH group at the end of the growing DNA chain acts as a

It attacks at the phosphorus adjacent tothe sugar in the nucleotide, which is added to the growing chain

nucleophile

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When the 3’ OH group of DNA attacks the phosphorus adjacent to the sugar, ___________ is eliminated,
and a new phosphodiester bond is formed.

Pyrophosphate

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four types of dNTP, or deoxynucleotide triphosphate

adenine (dATP), cytosine (dCTP), guanine (dGTP), and thymine (dTTP)

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a building block of DNA that’s used in DNA replication, sequencing, and more

A monomeric unit of DNA
Contains a nitrogen base, deoxyribose sugar, and three phosphate groups
Is made by reducing ribonucleotides with the enzyme ribonucleotide reductase

deoxynucleotide triphosphate

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which is a building block for RNA. rNTPs are made up of a ribose sugar, three phosphate groups, and a nitrogenous base.

They are also key metabolic energy carriers
They are substrates for many cell signaling pathway enzymes

rNTP stands for ribonucleotide triphosphate

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DNA is synthesized from its

5’ -> 3’ end

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this strand is synthesized continuously in the 5’ -> 3’ direction toward the replication fork

leading strand

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this strand is synthesized semidiscontinuously (Okazaki fragments) also in the 5’ -> 3’ direction, but away from the replication fork

lagging strand

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lagging strand fragments are joined by the enzyme

DNA ligase

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are enzymes that can act on templates to catalyze the hydrolysis of RNA substrates

Ribonuclease

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There are at least ____________ types of DNA polymerase (Pol) in E coli, ___________of which have been studied extensively

five

three

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DNA polymerase function has the following requirements:

all four deoxyribonucleoside triphosphates: dTTP, dATP, dGTP, and dCTP Cofactor: Mg2+ an RNA primer

a short strand of RNA to which the growing polynucleotide chain is covalently bonded in the early stages of replication

RNA primer

5 main elements of replication

all four deoxyribonucleoside triphosphates: dTTP, dATP, dGTP, and dCTP Cofactor: Mg2+ an RNA primer DNA pol DNA template

types of DNA polymerase repair and patching of DNA has exonuclease acitivity can do it both 5' to 3' and 3' to 5' activity

DNA-Pol I

types of DNA polymerase responsible for the polymerization of the newly formed DNA strand fastest turn over rate and biggest

DNA-Pol III

types of DNA polymerase proofreading and repair enzymes

DNA-Pol II, IV, and V

(class II topoisomerase) catalyzes reaction involving relaxed circular DNA

DNA gyrase

In prokaryotes, its an enzyme that creates a nick in relaxed circular DNA a slight unwinding at the point of the nick introduces supercoiling the nick is resealed

DNA gyrase

The energy required for this Supercoiling is supplied by the ___________ of ATP to ADP and Pi

hydrolysis

has different role in Replication with Supercoiled DNA. It introduces a nick in supercoiled DNA

DNA gyrase

Replication with Supercoiled DNA

DNA gyrase has different role here. It introduces a nick in supercoiled DNA a swivel point is created at the site of the nick the gyrase opens and reseals the swivel point in advance of the replication fork the newly synthesized DNA automatically assumes the supercoiled form because it does not have the nick at the swivel point

a helix-destabilizing protein, promotes unwinding by binding at the replication fork

helicase

stabilizes single-stranded regions by binding tightly to them

single-stranded binding (SSB) protein

What are the implications of Unwinding of the helix during DNA replication via helicase

Unwinding of the helix during DNA replication (by the action of helicase) results in supercoiling of the DNA ahead of the replication fork. This supercoiling increases with the progression of the replication fork. If the supercoiling is not relieved, it will physically prevent the movement of helicase.

catalyzes the copying of a short stretch of the DNA template strand to produce RNA primer sequence creates RNA that serves as a primer in DNA replication

Primase

the process by which primase synthesizes RNA primers that initiate DNA replication. primer activity first observed in-vivo.

Primase Reaction

how does the synthesis and linking of new DNA strands work

begun by DNA polymerase III the newly formed DNA is linked to the 3’-OH of the RNA primer as the replication fork moves away, the RNA primer is removed by DNA polymerase I

DNA Replication in Prokaryotes DNA synthesis is bidirectional.

true

DNA Replication in Prokaryotes The direction of DNA synthesis is from the _________ of the newly formed strand.

5’ end to 3’ end

DNA Replication in Prokaryotes __________ DNA polymerases have been found in E. coli.

Five

DNA Replication in Prokaryotes _________ introduces a swivel point in advance of the movement of the replication fork.

DNA gyrase

a point of rotation in DNA that allows one strand to pass through or around another. Swivel points are where enzymes break and reseal DNA bonds.

swivel point

DNA Replication in Prokaryotes The synthesis of new strands is catalyzed by _______.

Pol III

DNA Replication in Prokaryotes ____________ catalyzes the synthesis of an RNA primer.

Primase

Proofreading and Repair Errors in replication (mutations) occur spontaneously only once in every ___________ base pairs

10^9 to 10^10

Proofreading and Repair DNA replication takes place only ___________ each generation in each cell

once

the removal of incorrect nucleotides immediately after they are added to the growing DNA during replication

Proofreading

Errors in hydrogen bonding lead to errors in a growing DNA chain once in every _________ base pairs

10^4 to 10^5

Proofreading Improves Replication Fidelity

true

types of Proofreading enzymes recognize that two bases are incorrectly paired, the area of mismatch is removed, and the area replicated again

Mismatch repair

types of Proofreading catalyzed by Pol I: cutting is removal of the RNA primer and patching is incorporation of the required deoxynucleotides

Cut-and-patch

types of Proofreading Pol I removes RNA primer or DNA mistakes as it moves along the DNA and then fills in behind it with its polymerase activity

Nick translation

types of Proofreading a damaged base is removed by DNA glycosylase leaving an AP site; the sugar and phosphate are removed along with several more bases, and then Pol I fills the gap

Base excision repair

UV irradiation causes ____________ of adjacent thymine bases.

dimerization

When genetic information is rearranged to form new associations

Genetic Recombination

Oxygen radicals, in the presence of metal ions such as Fe21, can destroy sugar rings in DNA, breaking the strand.

Oxidation damage

in DNA Recombination, Reactions between homologous sequences are

Homologous

in DNA Recombination, Different nucleotide sequences recombine are

Nonhomologous

experiment demonstrated that a physical exchange of chromosome parts actually occurs during recombination.

Meselson and Weigle’s experiment

Method: They used two strains of lambda phage, one with "heavy" DNA labeled with a heavy isotope of nitrogen (N15) and the other with "light" DNA (N14), and infected bacteria with both strains simultaneously, allowing recombination to occur. Observation: By analyzing the density of the resulting phage progeny through density gradient centrifugation, they found that the recombinant phages had DNA densities intermediate between the heavy and light parental phages, indicating that DNA strands had physically broken and recombined to create new hybrid molecules.

proposed a model that accounted for heteroduplex formation and gene conversion during recombination.

Holliday model for homologous recombination.

Eukaryotic DNA Replication Cell growth and division divided into phases:

M, G1, S, and G2

The stages of mitosis and cell division defines what phase of the eukaryotic cell cycle

Not as understood as prokaryotic. Due in no small part to higher level of complexity.

Eukaryotic DNA Replication

is typically the longest part of the cell cycle, defines what phase of the eukaryotic cell cycle is characterized by rapid growth and metabolic activity

Cells that are quiescent—that is, not growing and dividing (such as neurons)—are said to be in what phase of the eukaryotic cell cycle

the time of DNA synthesis said to be in what phase of the eukaryotic cell cycle

a relatively short period of growth in which the cell prepares for division is said to be in what phase of the eukaryotic cell cycle

In Eukaryotic Replication, Best understood model for control of eukaryotic replication is from

yeast

DNA replication is initiated by chromosomes that have reached the _______ phase

G1 phase

The Biochemical Properties of Eukaryotic DNA Polymerases Nucleus 3' to 5' exonuclease - No Primase - Yes Processivity - Low Fidelity - High Replication - Yes Repair - No

a -DNA Polymerase

At least _______ different polymerases are present in eukaryotes _ have been studied more extensively

15 5

The Biochemical Properties of Eukaryotic DNA Polymerases Nucleus 3' to 5' exonuclease - Yes Primase - No Processivity - High Fidelity - High Replication - Yes Repair - ?

D -DNA Polymerase main DNA pol DNA pol III

The Biochemical Properties of Eukaryotic DNA Polymerases Nucleus 3' to 5' exonuclease - Yes Primase - No Processivity - High Fidelity - High Replication - Yes Repair - Yes

E -DNA Polymerase

The Biochemical Properties of Eukaryotic DNA Polymerases Nucleus 3' to 5' exonuclease - No Primase - No Processivity - Low Fidelity - Low Replication - No Repair - Yes

B -DNA Polymerase

The Biochemical Properties of Eukaryotic DNA Polymerases mitochondria 3' to 5' exonuclease - Yes Primase - No Processivity - High Fidelity - High Replication - Yes Repair - No

Gamma -DNA Polymerase

is the eukaryotic equivalent of the part of Pol III that functions as a sliding clamp ().

PCNA

Prokaryotes Five polymerases

polymerases (I, II, III, IV, V)

Eukaryotes Five polymerases

Five polymerases ( alpha, beta, gamma, epsilon, delta)

Prokaryote polymerase also a repair enzyme

DNA polymerase II

Prokaryote polymerase is involved in synthesis, proof reading, repair, and removal of RNA primers

DNA polymerase I

Prokaryote polymerase is the main polymerizing enzyme

DNA polymerase III

Prokaryote polymerase are repair enzymes under unusual conditions

DNA polymerase IV, V

Eukaryotes polymerase is a polymerizing enzyme

DNA polymerase a

Eukaryotes polymerase is a repair enzyme

DNA polymerase b

Eukaryotes polymerase is involved in mitochondrial DNA synthesis

DNA polymerase gamma

Eukaryotes polymerase is the main polymerizing enzyme

DNA polymerase delta

Eukaryotes polymerase is the leading strand replication enzyme

DNA polymerase epsilon

in prokaryotes, Polymerases are also exonucleases

true

in Eukaryotes, Not all polymerases are exonucleases

true

Eukaryotes or prokaryotes Okazaki fragments 1000–2000 residues long

prokaryotes

Eukaryotes or prokaryotes Okazaki fragments 150–200 residues long

Eukaryotes

Eukaryotes or prokaryotes No proteins complexed to DNA

prokaryotes

Eukaryotes or prokaryotes Histones complexed to DNA

Eukaryotes

Ends of eukaryotic chromosomes called are short (5 to 8 bp) tandemly repeated, G-rich nucleotide sequences that form protective caps 1-12 kbp long on the chromosome ends series of repeated DNA sequences

telomeres

Vertebrate telomere consensus sequence:

TTAGGG

(an RNA-dependent DNA polymerase) maintains telomere length by restoring telomeres at the 3'-ends of chromosomes

Telomerase

what cells that lack telomerase, inevitably lose bits of their telomeres

Somatic cells

what theory suggests that cells senesce and die when their telomeres are gone

telomere theory of aging

CHAPTER 10 Flashcards

(103 cards)