Replication of DNA Flashcards by VERNARD DOMINIC ALOYON

The DNA in the chromosomes carries out two functions:

It reproduces itself. This process is called
replication.
It supplies the information necessary to make all
the RNA and proteins in the body, including enzymes.

How well did you know this?

Not at all

Perfectly

The sequence of bases in DNA encodes _________

genetic information

How well did you know this?

Not at all

Perfectly

The duplication of DNA, giving rise to a new DNA molecule with the same base sequence as the original, is necessary whenever a cell divides to produce daughter cells. This duplication process is called __________

replication

How well did you know this?

Not at all

Perfectly

The actual formation of gene
products requires RNA; the production of RNA on a DNA template is called _______________

transcription

How well did you know this?

Not at all

Perfectly

The process by
which the base sequence directs the amino acid sequence is called ____________

translation

How well did you know this?

Not at all

Perfectly

In some viruses, RNA can direct its own synthesis as well as that of DNA. What enzyme____________ catalyzes this process.

reverse transcriptase

How well did you know this?

Not at all

Perfectly

Virus which RNA, rather than DNA, is the genetic
material.

retroviruses

How well did you know this?

Not at all

Perfectly

the cell also must protect the unwound portions of DNA from the action of __________ that preferentially attack single-stranded
DNA.

nucleases

How well did you know this?

Not at all

Perfectly

the mode in which DNA reproduces itself, such that
one strand comes from parent DNA and the other strand is newly formed

semiconservative replication

How well did you know this?

Not at all

Perfectly

the point at which the
DNA double helix begins to unwind at the start of replication

origin of replication

How well did you know this?

Not at all

Perfectly

in DNA replication, the
points at which new DNA strands are formed

replication forks

How well did you know this?

Not at all

Perfectly

A ___________ of newly synthesized DNA between regions of the original
DNA is a manifestation of the advance of the two replication forks in opposite directions.

“bubble”

also called an “eye”

How well did you know this?

Not at all

Perfectly

synthesis can take place in both directions from the origin of replication

bidirectional

How well did you know this?

Not at all

Perfectly

All synthesis of nucleotide chains occurs in the ________ from the perspective of the chain being synthesized.

5’ to 3’ direction

How well did you know this?

Not at all

Perfectly

Each gene is a section of a DNA molecule that contains a specific sequence typically comprising about

1000 to 2000 nucleotides.

How well did you know this?

Not at all

Perfectly

One of the syntheses is continuous along the 3’-to-5’ strand

leading strand

How well did you know this?

Not at all

Perfectly

Along the other strand that runs in the 5’¡3’ direction, the synthesis is discontinuous.

lagging strand

How well did you know this?

Not at all

Perfectly

carries the information necessary to produce one protein
or RNA molecule

base sequence of a gene

How well did you know this?

Not at all

Perfectly

The actual reaction occurring is a nucleophilic attack by the ________ of the deoxyribose of one nucleotide against the _________ on the 5’ carbon of the incoming nucleoside triphosphate

3’-hydroxyl
first phosphate

How well did you know this?

Not at all

Perfectly

DNA Replication steps

During replication, the very condensed superstructure of chromosomes must be opened so that it becomes accessible to enzymes and other proteins. What mechanism accomplishes this feat?

Opening Up the Superstructure

signal transduction mechanism

How well did you know this?

Not at all

Perfectly

DNA Replication steps

One notable step of the
signal transduction is the ________ and ________ of key lysine residues of histones.

Opening Up the Superstructure

acetylation and deacetylation

How well did you know this?

Not at all

Perfectly

DNA Replication steps

an enzyme, puts acetyl
groups on key lysine residues, some positive charges are eliminated and the strength of the DNA–histone interaction is weakened

. Opening Up the Superstructure

histone acetylase

How well did you know this?

Not at all

Perfectly

DNA Replication steps

removes these acetyl groups, the positive charges are reestablished. That, in turn, facilitates regaining the highly condensed structure of chromatin.

. Opening Up the Superstructure

histone deacetylase

How well did you know this?

Not at all

Perfectly

DNA Replication steps

are enzymes that facilitate the relaxation of supercoiling in DNA.

Relaxation of Higher-Order Structures of DNA

Topoisomerases
(also called gyrases)

How well did you know this?

Not at all

Perfectly

# DNA Replication steps The transient break forms a phosphodiester bond between a __________ of the enzyme and either the _____________ on the DNA. | Relaxation of Higher-Order Structures of DNA

- tyrosyl residue - 5' or 3' end of a phosphate

# DNA Replication steps are also involved in the untangling of the replicated chromosomes, before cell division can occur. | Relaxation of Higher-Order Structures of DNA

Topoisomerases

# DNA Replication steps Special unwinding protein molecules, called ______ attach themselves to one DNA strand and cause the separation of the double helix. | Unwinding the DNA Double Helix

helicases

# DNA Replication steps Helicases of eukaryotes are made of how many protein subunits? | Unwinding the DNA Double Helix

six

# DNA Replication steps How long are primers | Primers/Primases

4 to 15 nucleotides long

# DNA Replication steps RNA oligonucleotides synthesized from ribonucleoside triphosphates | Primers/Primases

Primers

# DNA Replication steps form complexes with DNA polymerase in eukaryotes. | Primers/Primases

Primases

# DNA Replication steps The enzyme catalyzing this synthesis of both daughter strands | Primers/Primases

Primases

# DNA Replication steps Primers are placed about every _______ in the lagging-strand synthesis. | Primers/Primases

50 nucleotides

# DNA Replication steps DNA Polymerase surrounds the end of the ___________, creating a specifically shaped pocket for the incoming nucleotide. | DNA Polymerase

DNA template– primer complex

# DNA Replication steps While the bases of the newly arrived nucleotides are being hydrogen-bonded to their partners, polymerases join the ____________ | DNA Polymerase

nucleotide backbones.

# DNA Replication steps Short DNA segments made of about 20 nucleotides in higher organisms eukaryotes) and of 2000 nucleotides in prokaryotes | DNA Polymerase

Okazaki fragments

# DNA Replication steps The Okazaki fragments and any nicks remaining are eventually joined together by another enzyme, | Ligation

DNA ligase

# Components of Replisomes and Their Functions Unwinds the DNA double helix

Helicase

# Components of Replisomes and Their Functions Synthesizes short oligonucleotides (primers)

Primase

# Components of Replisomes and Their Functions Allows the leading strand to be threaded through

Clamp protein

# Components of Replisomes and Their Functions Joins the assembled nucleotides

DNA polymerase

# Components of Replisomes and Their Functions Joins Okazaki fragments in the lagging strand

Ligase

# Components of Replisomes and Their Functions Protects the single-stranded regions from degradation during replication

Single-stranded binding protein (SSB)

the protein whose binding prepares for the start of DNA replication in eukaryotes

Replication activator proteins (RAP)

When a cell divides into two each of the two cells has one or has retained one of the original (template strands) and one of the new strands (daughter strands) that will partner with the leading strands through the complementary base pairing and now there will be 2 daughter DNAs

semi conservative replication

all synthesis of nucleotide chains occurs in the 5’ to 3’ direction from the perspective of the chain being synthesized.

semi discontinuous DNA replication

# The 5 DNA Polymerases in Prokayotes involved in proofreading and repair processes

DNA Polymerase 1 & 2

# The 5 DNA Polymerases in Prokayotes replaces the primer with deoxynucleotide (deoxy as it is in DNA and the sugar present is deoxyribose)

Polymerase 1

# The 5 DNA Polymerases in Prokayotes principal enzyme responsible for the synthesis of new DNA or new daughter strands of DNA and it is a multi-subunit enzyme

DNA Polymerase 3

# The 5 DNA Polymerases in Prokayotes Not studied extensively

DNA Polymerase 4 & 5

The primer and the protein at the replication fork as a whole are called

primosome

The entire complex including the DNA polymerase (important roles of DNA polymerase 1&3) is what you call the

replisome

In what phase of the Eukaryotic cell cycle does DNA Replication occur?

S phase

# 5 DNA polymerases 5 DNA polymerases in eukaryotes

- Alpha - Beta - Gamma - Theta - Epsilon

# 5 DNA polymerases Principal synthesizer of DNA and is equivalent to Polymerase III in prokaryotes.

Gamma

# . ERRORS IN DNA REPLICATION There is a fidelity in the binding of the base pairs. But there are occasions, due to tear and wear, where some _______ could happen during base-pairing, as well as in transcription and translation.

mutations

# . ERRORS IN DNA REPLICATION The viability of cells depends on ________ that can detect, recognize, and remove mutations from DNA

DNA repair enzymes

# . ERRORS IN DNA REPLICATION Externally, ________ or ________, may damage a base.

- UV radiation - highly reactive oxidizing agents (superoxide)

# . ERRORS IN DNA REPLICATION Errors in copying or internal chemical reactions, such as _________ can create damage internally

deamination of a base

# . ERRORS IN DNA REPLICATION Deamination of cytosine turns it into ______, which creates a mismatch.

uracil

# . ERRORS IN DNA REPLICATION One of the most common base repairs prepare means is called

BER (Base Excision Repair)

# . ERRORS IN DNA REPLICATION It is the job of Polymerase I and III, but sometimes during the proofreading by codons (by 3s), these commit mistakes | Kinds of Mutation

spontaneous mutation.

# . ERRORS IN DNA REPLICATION The result of error in natural biological processes. | Kinds of Mutation

SPONTANEOUS MUTATION

# . ERRORS IN DNA REPLICATION This mutation is due to chemical agents and could be physical agents in the environment that can cause change in the DNA structure | Kinds of Mutation

INDUCED MUTATION

# . ERRORS IN DNA REPLICATION Physical agents such as heat and UV radiation can cause this mutation | Kinds of Mutation

INDUCED MUTATION

# . ERRORS IN DNA REPLICATION UV is known to give ____________, so instead of the regular binding (A-T), it now becomes T-T, causing now an intercalation leading to the cancer of the skin. | Kinds of Mutation

thymine-thymine dimer

# . ERRORS IN DNA REPLICATION Chemical agents such as benzo-(a)-pyrene which you can get from the charred portion of broiled meat and fish can cause this mutation | Kinds of Mutation

INDUCED MUTATION

# . ERRORS IN DNA REPLICATION It is a good intercalating agent as it inserts into the DNA base-pairing. | Kinds of Mutation

benzo-(a)-pyrene

# . ERRORS IN DNA REPLICATION If it happens during S phase of the replication, then now you can perpetuate the mutations and can come up with different products. | Kinds of Mutation

benzo-(a)-pyrene

# . ERRORS IN DNA REPLICATION Due to oxidizing agents one of the commonest types of mutation would be _______ and _______ | Kinds of Mutation

depurination and deamination

# . ERRORS IN DNA REPLICATION (removal of the amino groups from the bases) of the pyrimidine and purine bases. | Kinds of Mutation

deamination

# . ERRORS IN DNA REPLICATION can be caused by depurination and deamination reaction. | Kinds of Mutation

Spontaneous mutation

# . ERRORS IN DNA REPLICATION is the kind of intervention of the glycosidic bond linkage due to chemical instability of the purine and pyrimidine bases. | Kinds of Mutation

Depurination

# BASE EXCISION REPAIR (BER) Important enzymes in part 1

1. DNA glycolase 2. Endonuclease 3. Exonuclease

# BASE EXCISION REPAIR (BER) Important enzymes in part 2

1. DNA polymerase 2. DNA ligase

# BASE EXCISION REPAIR (BER) Recognizes the damaged base and catalyzes hydrolysis of B-glycosidic bond between the base and deoxyribose.

DNA glycolase

# BASE EXCISION REPAIR (BER) The sugar-phosphate backbone here is still intact.

DNA glycolase

# BASE EXCISION REPAIR (BER) releases the damaged base completing the excision (like scissors)

DNA glycolase

# BASE EXCISION REPAIR (BER) cleaves the backbone at the AP (apurinic or apyrimidinic site)

Endonuclease

# BASE EXCISION REPAIR (BER) Helps in the excision repair of the sugarphosphate backbone to separate the apurinic and apyrimidinic site

Endonuclease

# BASE EXCISION REPAIR (BER) Liberates the sugar-phosphate unit of the damaged size.

Exonuclease

# BASE EXCISION REPAIR (BER) inserts the correct nucleotide, becoming an automatic repair system that detects the occurrence of a mutation and it instantaneously repair through the insertion of the correct nucleotide (such as cytidine for example)

DNA polymerase

# BASE EXCISION REPAIR (BER) seals the backbone to complete the repair

DNA ligase