DNA Replication 9

What does DNA stand for?

Deoxyribonucleic acid.

What does RNA stand for?

Ribonucleic acid.

What is the primary function of DNA in cells?

DNA serves as chemical information used by cells in constructing, managing, and maintaining itself.

What is true about the next generation of cells when derived from previous generations?

The next generation of cells will be structurally and physiologically like the previous generation will be malleable

Can DNA self-replicate?

No, DNA cannot self-replicate.

What must occur before a cell divides?

It must duplicate all of its DNA molecules to ensure that each new cell has the correct amount of chemical instructions.

What process takes place to duplicate DNA before cell division?

The two strands of DNA separate so that enzymes can access, duplicate the strands, and prepare them for separation during division.

What is deoxyribose sugar?

A pentose (5-carbon) sugar with a hydrogen (H+) at the 2' carbon position, missing an oxygen (O2) atom.

What does 'deoxy' refer to in deoxyribose?

'Deoxy' means that the sugar is missing an oxygen atom at the 2' position.

What is ribose?

A pentose (5-carbon) sugar with a hydroxyl (OH-) group at the 2' carbon position.

How many DNA molecules do humans have?

Humans have 46 DNA molecules, with 23 inherited from each parent.

What is Chargaff's rule?

Chargaff's rule states that in a DNA strand, the amount of adenine (A) is equal to thymine (T), and cytosine (C) is equal to guanine (G).

If a DNA molecule has 20% adenine, what percentage of thymine does it have?

It will also have 20% thymine due to Chargaff's rule.

How do nitrogenous bases interact in DNA?

Nitrogenous bases in the parallel strands of DNA form hydrogen bonds to create the double helix structure.

What is the structure of DNA?

DNA is structured as a double helix, formed by two complementary antiparallel strands.

What are the three hypothesized ways how DNA strands can split?

Conservative replication, dispersive model, and semiconservative model.

What is the conservative replication model?

In the conservative replication model, each original parent strand forms a new strand, remaining together while forming a new molecule with two new strands. Same 2 old parent strands

What does the dispersive model of DNA replication entail?

Each new molecule contains individualized sequences from both the original parent strands and the newly replicated strands, with neither parental strand being conserved.

What is the semiconservative model of DNA replication?

Each new DNA molecule gets one original parent strand and one newly synthesized strand, allowing for the conservation of one strand from the parent.

How do DNA strands separate during semiconservative replication?

Hydrogen bonds between the two strands break, allowing them to unwind and separate, with each strand acting as a template for the synthesis of a new strand.

What is the significance of the semiconservative model in DNA replication?

All life replicates its DNA using the semiconservative model, ensuring each daughter double helix has one old strand and one new strand.

What is the double helix model of DNA?

The double helix model consists of two polynucleotide chains twisted around each other, resembling a double spiral staircase.

What does it mean that the two chains of DNA are antiparallel?

Antiparallel means that the two chains run in opposite directions, exhibiting opposite polarity.

What fills the central space of the double helix?

Pairs of nitrogenous bases fill the central space of the double helix.

What did scientists initially believe was the hereditary molecule before DNA?

Scientists once believed that proteins were the hereditary molecules before the discovery of DNA.

What is a nucleoside?

A nucleoside is a molecule made of a nitrogenous base and a pentose sugar, without a phosphate group.

What are the four different nucleotides found in DNA?

The four nucleotides in DNA contain one deoxyribose sugar, one phosphate group, and one of the four nitrogenous bases: A, G, T, or C.

What are purines and which bases fall under this category?

Purines are nitrogenous bases that have a two-ring structure; adenine (A) and guanine (G) are purines.

What are pyrimidines and which bases are classified as pyrimidines?

Pyrimidines are nitrogenous bases that have a single-ring structure; thymine (T), cytosine (C), and uracil (U) are pyrimidines.

How are complementary bases paired in DNA?

A purine pairs with a pyrimidine through hydrogen bonds, specifically A-T pairs have 2 hydrogen bonds, while G-C pairs have 3 hydrogen bonds.

What is the order of nucleotide mass from highest to lowest?

The order from highest to lowest mass is guanine (G), adenine (A), cytosine (C), thymine (T).

What is the sugar-phosphate backbone of DNA?

The sugar-phosphate backbone is formed by linking deoxyribose sugars with alternating phosphate groups, creating a structural framework for DNA.

How does a phosphate group connect two deoxyribose sugars?

A phosphate group links the 3’ carbon of one sugar to the 5’ carbon of the next sugar, forming a phosphodiester bond.

What is bound to the 5' carbon of a deoxyribose sugar?

A phosphate group is bound to the 5' carbon of a deoxyribose sugar, marking the 5' end of the DNA strand.

What is bound to the 3' carbon of a deoxyribose sugar?

A hydroxyl group is bound to the 3' carbon of the deoxyribose sugar, marking the 3' end of the DNA strand.

What is a phosphodiester linkage?

A phosphodiester linkage is a covalent bond that connects nucleotides in a DNA or RNA strand.

What role do nucleotide triphosphates play in DNA formation?

Nucleotide triphosphates provide the energy needed for bond formation during nucleic acid synthesis.

How does the negative charge of phosphate groups affect DNA structure?

The negative charge of phosphate groups causes them to repel each other, contributing to the instability and raising the potential energy of the polynucleotide chain.

What does it mean for a polynucleotide chain to have polarity?

Polarity in a polynucleotide chain refers to the distinct 5' and 3' ends, which affects strand orientation and nucleotide interaction.

What is X-ray diffraction used for in studying DNA?

X-ray diffraction involves directing an X-ray beam at a molecule, revealing an X pattern that represents the helical structure of DNA.

How is DNA stored in eukaryotic cells?

In eukaryotic cells, DNA is wrapped around histone proteins into clusters called nucleosomes, which coil into chromatin.

What is the central dogma of molecular biology?

The central dogma describes the flow of genetic information: DNA is transcribed into mRNA, which is then translated into a polypeptide, forming proteins.

What are DNA polymerases?

DNA polymerases are enzymes responsible for synthesizing DNA by linking nucleotides together to form a new strand during DNA replication.

Which end of the existing DNA chain do DNA polymerases add nucleotides to?

DNA polymerases add nucleotides only to the 3’ exposed hydroxyl group of the existing chain.

What are the four different deoxyribonucleotide triphosphates involved in DNA synthesis?

The four deoxyribonucleotide triphosphates are dATP, dGTP, dCTP, and dTTP, each corresponding to one of the DNA bases.

In which direction do DNA polymerases assemble nucleotide chains?

DNA polymerases assemble nucleotide chains in the 5’ to 3’ direction; however, the template strands are read in the 3’ to 5’ direction.

What indicates the newest end of a newly synthesized DNA strand?

A 3’ -OH group is exposed at the newest end of a newly synthesized DNA strand, while the oldest end has an exposed triphosphate.

What is DNA polymerase III?

DNA polymerase III is the main polymerase enzyme that adds nucleotides only to the 3’ end of a growing DNA strand during replication.

What is the role of DNA polymerase I?

DNA polymerase I plays a role in the formation of the lagging strand by removing RNA primers and replacing them with DNA nucleotides.

What do RNA polymerases do?

RNA polymerases synthesize RNA from a DNA template by reading the DNA and creating a complementary RNA strand, which is essential for protein synthesis.

What is the function of primase?

Primase is an enzyme that synthesizes RNA primers to initiate DNA replication by providing a starting point for DNA polymerases.

What are primers in DNA replication?

Primers are short RNA sequences that serve as starting points for DNA polymerization during the replication process.

What is the role of the sliding DNA protein clamp?

The sliding DNA protein clamp binds to DNA polymerase, preventing it from dissociating, which increases rate of DNA synthesis.

What does helicase do during DNA replication?

Helicase is an enzyme that unwinds the DNA double helix by breaking hydrogen bonds between base pairs, creating a fork shape for replication.

What is the purpose of single-stranded binding proteins (SSB)?

Single-stranded binding proteins coat and stabilize unraveled DNA strands during replication, preventing them from re-annealing.

What is the function of topoisomerase?

Topoisomerase is an enzyme that relieves tension in the DNA helix by cutting and rejoining DNA strands to prevent excessive twisting during replication.

What role does primase play in DNA synthesis?

Primase synthesizes small sequences of RNA primers that bind to parent strands, allowing DNA polymerases to begin polymerization.

How are the leading and lagging strands synthesized differently?

The leading strand is synthesized continuously in the direction of unwinding, while the lagging strand is synthesized in short segments called Okazaki fragments, discontinuously opposite to unwinding.

What is the purpose of ligase in DNA replication?

Ligase is an enzyme that fuses bonds together between DNA monomers by forming phosphodiester bonds, and it specifically binds Okazaki fragments together.

What is meant by the continuous and discontinuous replication of DNA?

The leading strand undergoes continuous replication, while the lagging strand undergoes discontinuous replication due to the need for multiple RNA primers.

What is a replication bubble?

A replication bubble is formed when helicase unwinds the DNA, creating fork-like structures at the sites of replication.

In which direction is DNA synthesized during replication?

DNA is synthesized from the 5' to 3' direction, occurring simultaneously in both the leading and lagging strands during replication.

What is the function of telomerase?

Telomerase prevents the shortening of telomeres by adding telomere repeats to the ends of chromosomes during DNA replication.

What is a telomere?

A telomere is a noncoding buffer at the ends of eukaryotic chromosomes composed of short, repeating DNA sequences that protect the chromosome.

What happens when the RNA primer is removed from a newly synthesized DNA strand?

When the RNA primer is removed, a gap is left at the 5’ end of the new DNA strand that DNA polymerase cannot fill due to the antiparallel nature of DNA strands.

How does telomerase contribute to DNA replication in adult cells?

In adults, telomerase is primarily active in rapidly dividing embryonic cells, germ cells, and cancerous somatic cells, allowing the maintenance of telomere length.

What role does the RNA section of telomerase serve?

The RNA section of telomerase acts as a template for the addition of telomere repeats to chromosome ends during DNA synthesis.

What occurs when the buffering by telomeres fails?

Buffering fails when the entire telomere is lost, which can lead to chromosome instability and cell aging or death.

What is proofreading in DNA replication?

Proofreading is a process where DNA polymerase III checks and corrects its own errors during DNA replication by going back one base pair to fix mismatched nucleotides.

What is the function of exonuclease activity in DNA polymerases?

Exonuclease activity allows DNA polymerases to remove incorrectly added nucleotides during DNA synthesis and replace them with the correct ones, resuming forward synthesis afterwards.

What are distortions in DNA structure and what causes them?

Distortions are changes in molecular shape in DNA structure caused by mispaired bases during replication, which can interfere with normal DNA function.

What do mismatch repair enzymes do after DNA replication?

Mismatch repair enzymes cut the new DNA strand on each side of a mismatch, remove the erroneous nucleotides, and allow DNA polymerase to fill in the gap with the correct DNA.

What is the role of DNA ligase in DNA repair?

DNA ligase seals the nucleotide chain after the erroneous nucleotides have been removed and replaced through DNA polymerase, ensuring the continuity of the DNA strand.

What does base-excision repair address?

Base-excision repair addresses nonbulky DNA damage by removing and replacing erroneous bases based on complementary pairing rules to restore proper DNA structure.

What type of damage does nucleotide-excision repair fix?

Nucleotide-excision repair fixes bulky distortions in DNA, such as thymine dimers, by removing an entire segment of damaged DNA and synthesizing new DNA.

What can happen if errors remain after DNA repair mechanisms?

Errors that remain after proofreading and repair mechanisms can result in mutations, which may alter the functioning of proteins and potentially lead to lethal outcomes for the organism.

What are the two main types of mutations that can alter protein structure?

Base-pair substitutions and chromosomal mutations.

What is a missense mutation?

A missense mutation is a base-pair substitution that changes an mRNA codon to a different sense codon, specifying a different amino acid.

What is a nonsense mutation?

A nonsense mutation occurs when a nucleotide base pair is changed, resulting in a premature stop codon in the DNA sequence, leading to truncated proteins.

What is a silent mutation?

(Base pair) A silent mutation is a change in the nucleotide sequence that does not result in a change in the amino acid sequence of the protein encoded by that gene.

What is a frameshift mutation?

(Base pair) A frameshift mutation happens when nucleotides are inserted or deleted from the DNA sequence, altering the reading frame and resulting in changes to the entire amino acid sequence downstream.

What are chromosomal mutations?

Chromosomal mutations are alterations that affect entire chromosomes or whole genes, rather than just individual nucleotides. (Duplications, inversions, deletions, translocations, insertions)

What is a duplication mutation?

A duplication mutation occurs when a portion of genetic material or a chromosome is duplicated, resulting in multiple copies of that region.

What are inversions in the context of chromosomal mutations?

Inversions occur when a segment of a chromosome breaks off and is reinserted in the reverse direction relative to the rest of the chromosome.

What are deletions in chromosomal mutations?

Deletions result when one or a few nucleotide base pairs are lost from a chromosome, often causing large changes in the reading frame of the DNA.

What are translocations regarding chromosomal mutations?

Translocations involve the movement of a chromosomal segment from one position to another, either within the same chromosome or to a different chromosome.

What is an insertion mutation?

An insertion mutation is characterized by the addition of one or a few nucleotide base pairs into a DNA sequence or chromosome, which can be small or large scale.

What are transposons?

Transposons are repetitive DNA sequences that can move (transpose) from one location to another within the genome.

What are some effects of transposon movement?

Transposon movement can result in mutations, alter gene expression, induce chromosome rearrangements, and increase genome sizes due to elevated copy numbers.

What is transposition in genetics?

Transposition is a type of genetic recombination where transposons move to a new location in the genome, typically involving a target site that is not homologous.

What are the two mechanisms of transposition?

The two mechanisms of transposition are:
1) Cut and paste, where the transposable element (TE) leaves its original location (moves from one spot to another);
2) Copy and paste, where a copy of the TE moves to a new location while the original remains (stays in same place and goes to another spot)

Who first discovered transposons?

Transposons were first discovered by geneticist Barbara McClintock.