Dna Synthesis And Replication

Front 1

Name the 3 parts of a nucleotide.

Back 1

-deoxyribose sugar
-one phosphate group attached to the sugar
-a nucleoside or base: A, T, C, and G

Front 2

What type of bonds link nucleotides or ribonucleotides?

Back 2

covalent bonds between sugar and phosphate

Front 3

What type of bonds link the bases to create a double helix?

Back 3

hydrogen bonds

Front 4

Name characteristics of DNA.

Back 4

-Long, double-stranded molecules of DNA.
-Always unbranched
-Same four monomers: A, T, C, and G.

Front 5

What is required of the template strand?

Back 5

Replication requires a template strand of DNA. Strand must be free or unpolymerized (hydrogens broken and bases exposed)

Front 6

What is a semiconservative replication?

Back 6

Each DNA strand is used to synthesize a new double stranded molecule of which it makes up one-half.

Front 7

What direction does DNA polymerase read a strand?

Back 7

5' to 3'

Front 8

What is the leading strand?

Back 8

the strand that is continuously polymerized in the 5' to 3' direction

Front 9

What is semiconservative replication?

Back 9

Front 10

What does a strand of DNA look like at the molecular level?

Back 10

Front 11

What does it mean that Double stranded DNA runs antiparallel?

Back 11

one side of the replication fork is moving in s 3' to 5' direction at all times.

Front 12

Can DNA synthesis begin de novo?

Back 12

Nothe DNA polymerase requires a primer to begin synthesis.
RNA synthesis, however, can begin de novo
intermediate RNA molecules serve as DNA synthesis primers.

Front 13

What types of proof reading methods are used when replicating DNA?

Back 13

-Several methods of proofreading occur from the DNA polymerase itself.
-The correct nucleotide has higher affinity for the polymerase because the reaction is energetically favorable.
-When the nucleotide is bound to the DNA polymerase, the enzyme undergoes a conformational change in order to covalently link it to the previous nucleotide.

Front 14

How many primers are required for the lagging strand?

Back 14

For the lagging strand, one primer is required for every Okazaki fragment

Front 15

What is required to initiate synthesis of DNA?

Back 15

an RNA primer

Front 16

How many primers are required for the leading strand?

Back 16

One

Front 17

What is DNA primase?

Back 17

DNA primase
synthesizes short (10bp) RNA primers on DNA templates
Results in a DNA:RNA hydrogen-bound hybrid molecule.

Front 18

What does DNA polymerase do after DNA primase performs its actions?

Back 18

DNA polymerase elongates the RNA primer from the 3’-OH end.

Front 19

DNA primase and polymerase

Back 19

Front 20

What happens when DNA reaches the 5' end of a primer?

Back 20

It falls off
Creates a hanging single-stranded ribonucleoside which is then Recognized by specialized proteins which remove the RNA primer.
DNA ligase then extends the DNA strand
from the 3’ end of the new DNA fragment to the 5’ end of the latest DNA fragment.

Front 21

Once RNA primer is removed what does DNA ligase do?

Back 21

extends the DNA strand from the 3' end of the new DNA fragment to the 5' end of the latest DNA fragment essentially gluing the 2 pieces together.

Front 22

The DNA polymerase and DNA ligase in action

Back 22

Front 23

Name proofreading mechanisms.

Back 23

-Incorrect nucleotide addition
At the end of a primer strand will result in that nucleotide remaining unpaired.
-There is a separate catalytic site on the DNA polymerase, responsible for exonucleolytic proofreading
-It will recognize this unpaired 3’-OH end as incorrect and excise the unpaired nucleotides until a correctly base-paired 3’-OH remains.

Front 24

At what end is it possible to correct mistake in nucleotide addition?

Back 24

3’-OH end.

Front 25

What isn't it possible to excise or correct a mistake in nucleotide addition from the 5' end?

Back 25

The 5' end would result in a nucleoside monophosphate at the terminus

No further reaction could proceed because the cleavage of a high energy nucleoside triphosphate bond is required for polymerization.

Front 26

What is DNA helicase?

Back 26

-an enzyme which rapidly moves along a single strand of DNA ahead of the replication machinery
utilizes ATP hydrolysis to break hydrogen bonds between annealed DNA strands thereby opening the replication fork.

Front 27

What happens after helicase has uncovered a DNA strand?

Back 27

Single-strand binding proteins (SSB) bind to the DNA and
aid the helicase in stabilizing the unwound DNA without covering the bases enough to impede templating.

Front 28

What is the purpose of a sliding clamp and where does it bind?

Back 28

-binds to the back of the DNA polymerase and forms a ring around the DNA molecule.
-prevents the DNA polymerase from frequently falling off
-clamp is assembled on the DNA before the polymerase binds it
via a clamp loader which requires ATP.
-There is one pre-loaded clamp for every RNA primer.

Front 29

What is a sliding clamp?

Back 29

A sliding clamp
Binds the back of the DNA polymerase and forms a ring around the DNA molecule.

Front 30

Where does a sliding clamp bind and when does it bind?

Back 30

Binds to the black of the DNA polymerase and forms a ring around the DNA molecule.
The clamp is assembled on the DNA before the polymerase binds it via a clamp loader

Front 31

What is the purpose of a sliding clamp?

Back 31

preventsthe DNA from frequently fall off

Front 32

Does a sliding clamp use energy to bind?

Back 32

Yes, ATP

Front 33

How many clamps does each RNA primer use?

Back 33

one

Front 34

All of these proteins function as a rapid multienzyme complex, therefore, their actions must be thought of as coupled together.

Back 34

-DNA helicase opens the DNA helix at the front of the replication fork.
-SSB proteins bind the single strand to prevent re-annealing or hairpin loops.
-The DNA polymerase of the leading strand operates continuously at the replication fork with the assistance of a sliding clamp.
-The DNA polymerase of the lagging strand restarts at short intervals using the discontinuous assistance of a DNA primase
to create RNA primers and a clamp loader to pre-load a sliding clamp to each primer.
-The replication fork is followed by the enzymes responsible for primer excision and DNA ligase.

Front 35

What is DNA topoisomerase I?

Back 35

-reversibly break phophosdiester bonds
-allows double helix to swivel and relieve tension
-Creates and then reseals a single-strand break in the backbone of the double-stranded DNA ahead of the replication fork
-Allows both sections of the single strand to rotate freely
-uses built up tension and the other strand as a swivel point.

Front 36

What is DNA topoisomerase II?

Back 36

-Creates and then reseals a double-strand break
-This allows a separate DNA molecule crossing over the first to pass through unobstructed.

Front 37

What is a replication origin and what type of bases are these areas usually rich in?

Back 37

Sites at which DNA strands are first separated
Usually AT rich because easier to open.
RNA primer synthesis then takes place.

Front 38

What is the function of initiator Proteins?

Back 38

assist in initiating replication by breaking hydrogen bonds to separate strands of DNA.

Front 39

Are replication origins activated in clusters and how many units apart are they?

Back 39

-activated in clusters
-Origins of Replication are thousands of nucleotides apart.
-Replication forks always open in pairs (Replication Bubbles)
-DNA Synthesis always occurs during S phase

Front 40

What is the prereplicative complex?

Back 40

Once helicase loading proteins (Cdc6 and Cdt1) are produced, they bind the origin of recognition complex-DNA to form the prereplicative complex

Front 41

Through what time in the cell cycle of eukaryotic cells is the origin of recognition complex bound?

Back 41

bound through most of the cell cycle

Front 42

What triggers the passage from G1 to the S phase of cell cycle?

Back 42

Cdks (protein kinases phosphyorylating other proteins) are activated which then dissociate the helicase loading protein.
In turns activates helicase which then unwinds DNA at the origin.
DNA polymerases and the remaining replication proteins are then loaded.

Front 43

What is found in the replication fork?

Back 43

the replication machinery

Front 44

Does eukaryotic DNA or prokaryotic DNA replicate more slowly? And why?

Back 44

eucaryotic
-activated in clusteres called replication units
-individual orgines of replication are spcaed tens of thousands of nucleotides apart
-replication forks always open in pairs, creating replication bubbles
DNA synthesis always occurs during the S phase of the cell cycle and the entire genome is completely replicated
-replication units are activated at distinct times throughout S phase and heterochromatin is replicated late in S phase suggesting chromatin condensation is related to timing of replication

Front 45

What bases does the origin recognition complex bind to initiate replication in yeast and prokaryotes?

Back 45

mostly As and Ts

Front 46

How many histones are required after replication?

Back 46

Equal amounts of new histones as DNA mass are required after replication.

To solve this, humans have about 20 copies of each histone gene from which protein is synthesized in S phase.

Front 47

What type of proteins assist replication forks in moving through parental nucleosomes without displacing them?

Back 47

chromatin-remodeling proteins

Front 48

Give an example of epigenetic inheritance.

Back 48

refers to heritable traits which occur wihtout changes in a nucleotide sequence, histones are one example

Front 49

List the roles of chromatin-remodeling proteins

Back 49

-Assist the replication forks in moving through parental nucleosomes.
-facilitates nucleosomes distribution to each daughter strand.
-Allows for epigenetic inheritance:
Heritable traits which occur without changes in nucleotide sequence.
Modification of H3 and H4 (example: Methylation)

Front 50

Describe histone replication.

Back 50

After Replication:
-Equal amounts of histone protein as DNA needed.
-Synthesized in S phase from 20 copies of each histone gene.
-Histone chaperones bind basic histones and distribute them to fill in holes.

Front 51

Why does telomerase exist.

Back 51

No room to produce RNA primer for last lagging strand, telomeres are segments of DNA at the end of linear strands, composed of many repeating bases.

Front 52

What does telomerase do?

Back 52

enzyme which recognizes the telomere sequence and elongates it after each cell division, elongates in 5' to 3' direction, utilizes an RNA subunit. Purpose is to protect the overhang from degredation.

Front 53

What has indefinite polymerase activity?

Back 53

yeast

Front 54

What happens each time a cell divides to telomerase?

Back 54

Cells lose telomerase through each divison.
Eventually cells become senescence.

Front 55

What is senescence?

Back 55

means that cells can no longer divide due to defects near the ends of chromosoms

Front 56

What is the Hayflick limit?

Back 56

cells have a limited life span

Front 57

What are the HeLa cells?

Back 57

cells cultured from Henrietta Lacks who died of cervical cancer, immortal cell line that was used to develop the polio vaccine.

Front 58

Explain the reasons for cell senescence and immortalization.

Back 58

with every cell division, telomerase is lost, eventually cells become senescence.
immortalization can occur if telomerase production is indefinite.

Front 59

How many nucleotides are lost each time a cell divides?

Back 59

100-200