BB 451 DNA replication

What is the difference between Ribonucleotide and Deoxyribonucleotide?

Ribonucleotides are the building blocks of RNA, characterized by the presence of a hydroxyl group (-OH) on the 2' position of their sugar, ribose. In contrast, deoxyribonucleotides, which form DNA, have a hydrogen atom (H) at the 2' position, providing additional chemical stability to DNA compared to RNA.

Why is DNA more stable than RNA?

DNA exhibits greater chemical stability than RNA largely due to the absence of the 2' hydroxyl group found in ribonucleotides. This absence makes DNA less prone to hydrolysis, thus preserving genetic information more reliably.

What are the components of DNA?

The structure of DNA comprises four nitrogenous bases: two purines—Adenine (A) and Guanine (G)—and two pyrimidines—Cytidine (C) and Thymidine (T). These bases participate in specific hydrogen bonding patterns across the two strands, forming the genetic code.

What are the ends of a DNA strand called?

Each DNA strand possesses a specific orientation; the 5’ end, which terminates with a phosphate group attached to the fifth carbon of the sugar, allows for the initiation of DNA synthesis, while the 3’ end has a hydroxyl group (-OH) attached to the third carbon.

What bonds hold DNA together?

DNA’s backbone is constructed through phosphodiester bonds, which are covalent connections formed between the phosphate of one nucleotide and the hydroxyl of the sugar of another, establishing the sugar-phosphate backbone fundamental to its structure.

In which direction does DNA synthesis occur?

DNA synthesis is directed strictly from the 5' end to the 3' end, meaning that nucleotides are always added to the 3' hydroxyl (-OH) group of the existing strand.

What is the significance of the antiparallel structure of DNA?

In the antiparallel structure of DNA, the two strands run in opposing orientations; one strand is oriented 5’-3’ while its complementary strand runs 3’-5’. This arrangement is critical for the proper pairing of bases.

What is the strength of hydrogen bonding in DNA bases?

The hydrogen-bonding strength in DNA base pairs contributes to its stability; Guanine and Cytosine (G-C) pairs form three hydrogen bonds, making them stronger and more stable than Adenine and Thymine (A-T) pairs, which only form two hydrogen bonds.

What is the most common form of DNA?

The most prevalent configuration of DNA in living organisms is the B-form, characterized by a right-handed helix. Other forms include A-form and Z-form.

What are major and minor grooves in DNA?

Major and minor grooves are structural features of the DNA double helix, where the sugar-phosphate backbone is not evenly spaced, providing binding sites for proteins essential for genetic processes.

How many base pairs are there per turn in B-DNA?

In the B-form of DNA, there are approximately 10.5 base pairs per complete helical turn.

How is DNA compacted in cells?

DNA is compacted within eukaryotic cells through interactions with histone proteins, which package DNA into a condensed structure called chromatin.

What is semiconservative replication?

Semiconservative replication refers to the mechanism by which DNA is replicated, where each newly formed double helix consists of one original strand and one newly synthesized strand.

What is the role of DNA polymerase?

DNA polymerase is a key enzyme involved in DNA replication, responsible for synthesizing new DNA strands by adding nucleotides complementary to the template strand.

How do leading and lagging strands differ?

The leading strand is synthesized continuously as the replication fork opens, while the lagging strand is synthesized discontinuously in fragments known as Okazaki fragments.

What is the purpose of the RNA primer in DNA replication?

The RNA primer is a short RNA strand synthesized by the enzyme primase, providing a necessary starting point for DNA polymerase to begin nucleotide addition.

What are Okazaki fragments?

Okazaki fragments are short sequences of DNA synthesized on the lagging strand during DNA replication.

In which direction does DNA polymerase synthesize DNA?

DNA polymerase synthesizes DNA in the 5' to 3' direction by adding nucleotides to the 3’ hydroxyl (-OH) end of the growing chain.

What is DNA elongation?

DNA elongation is the part of DNA replication where nucleotides are added one by one to the existing strand.

What is proofreading in DNA synthesis?

Proofreading is an essential function of DNA polymerase, utilizing its 3’-5’ exonuclease activity to identify and excise incorrectly paired nucleotide bases.

What are the key proteins involved in DNA replication?

Key proteins involved in DNA replication include DNA polymerase, helicase, single-stranded binding proteins (SSBs), primase, topoisomerase, ligase, and sliding clamp proteins.

What is the function of the replication fork?

The replication fork is where the DNA double helix is unwound to allow for synthesis of new strands.

What role does DNA polIII play in bacteria?

In bacteria, DNA polymerase III is responsible for elongation and has exonuclease activity.

What does topoisomerase do?

Topoisomerase alleviates torsional strain from DNA unwinding during replication.

What is the rate of bacterial DNA replication?

Bacteria replicate their DNA every 20 minutes.

What are the types of topoisomerase?

There are two types: Type 1 topoisomerase cuts one DNA strand, while type 2 (gyrase) cuts both strands.

What is the function of single-stranded binding proteins (SSBs)?

Single-stranded binding proteins prevent re-annealing of DNA strands during replication.

What role does the sliding clamp play?

The sliding clamp enhances DNA polymerase's processivity by tethering it to the DNA template.

How is a phosphodiester bond formed?

A phosphodiester bond forms when the oxygen from a hydroxyl group attacks the phosphate group.

What is the function of DNA polI?

DNA polI removes RNA primers using 5’-3’ exonuclease activity and fills in the gaps with DNA.

Why is supercoiled DNA important?

Supercoiling compactifies DNA, and topoisomerase can generate supercoiling.

What is the linking number equation?

Linking number = twist + writhe; twist = number of turns, writhe = crossings of the double helix.

What are the steps in the Polymerase Chain Reaction (PCR)?

replicates desired stretch of DNA from trace amounts (amplification)

1. separate strands of DNA by heating mixture to near boiling (breaks hydrogen bonds)

2. Add in DNA primers (synthetically made) to flank region of interest and lower temperature so they will attach to DNA

3. warm mixture to allow replication to occur (Taq polymerase special, can survive high heat)

repeat process for 30-40 cycles

How do prokaryotic and eukaryotic replication differ?

Prokaryotic Replication	Eukaryotic Replication
This process occurs in prokaryotic cells.	This process occurs in eukaryotic cells.
It is a continuous process.	This process occurs in the S-phase of the cell cycle.
Circular, double-stranded DNA	Linear, double-stranded DNA with end
The DNA replicates in the cytoplasm	The DNA replicates in the nucleus
Single origin of replication	Multiple origins of replication
Small amount of DNA	The DNA is 50 times more than prokaryotic DNA
DNA polymerase I and III are involved	DNA polymerase ɑ, δ and ε are involved.
Large okazaki fragments	Small okazaki fragments
The process is rapid, 2000 base pairs per second	The process is slow, 100 base pairs per second
Two circular chromosomes are obtained	Two sister chromatids are obtained
DNA gyrase is required	DNA gyrase is not required

What are the functions of multiple replication forks?

Eukaryotes have multiple replication forks to efficiently replicate larger genomes.

What is the origin of replication ('oriC')?

The oriC is a specific DNA sequence recognized by proteins to initiate replication.

How long does eukaryotic DNA replication take?

Eukaryotic cells typically take about 24 hours to replicate their DNA.

Why are A-T rich origins significant?

Origins rich in A-T pairs require less energy to separate due to only two hydrogen bonds.

What is the linear chromosome end problem?

Linear chromosomes may lose DNA at the ends during replication, addressed by telomeres.

What happens during the mutation repair process?

Incorrect bases are removed or repaired; if repair fails, cells may undergo apoptosis.

What causes thymine dimers and how are they repaired?

Thymine dimers result from UV radiation, causing covalent bonding; repaired by photolyase.

What is nucleotide excision repair?

Nucleotide excision repair involves cutting out damaged DNA sections for repair.

What is base excision repair?

Base excision repair removes incorrect bases, such as uracil, not normally found in DNA.

What is the result of cytosine deamination?

Cytosine deaminates to uracil, which pairs with adenine instead of guanine.

What role does uracil-N-glycosylase play?

Uracil-N-glycosylase removes uracil from DNA to prevent mispairing.

What is DNA mismatch repair?

Mismatch repair detects and corrects errors in base pairing during DNA replication.

What causes bulges in DNA?

Bulges in DNA are caused by improper base pair matches.

How is a mismatch identified?

The old methylated strand is recognized as correct, allowing the cell to identify mismatches.

When does recombination occur?

Recombination occurs during prophase I of meiosis.

What is a tetrad?

A tetrad consists of two homologous chromosomes.

What is synapsis?

Synapsis is the pairing of homologous chromosomes to form a tetrad.

What is a chiasma?

A chiasma is the site where two chromosomes overlap during meiosis.

What is the synaptonemal complex?

The formation of the synaptonemal complex allows genetic material exchange at the chiasma.

What is crossing over?

Crossing over refers to the exchange of genetic material between chromosomes.

Why is genetic recombination important?

Genetic recombination increases genetic diversity, influencing evolution through allele shuffling.