BIOL 329: DNA Replication and Repair, Chromatin and Chromosomes, Cell Cycle

Flashcards covering DNA replication and repair mechanisms, chromatin structure, chromosome organization, and key cell cycle events based on the provided lecture notes. Presented in a question-and-answer format for exam preparation.

What is continuously needed to keep polymerization going on the lagging strand?

A primer (strand primer).

What is the function of DNA polymerase (repair polymerase) in replication?

It replaces primers with DNA.

What enzyme joins the 5' end of DNA to the 3' hydroxyl end of the next Okazaki fragment?

DNA ligase.

What is the role of helicase in DNA replication?

It unravels DNA and leads replication at the fork.

What do single-strand DNA-binding proteins (SSDB) prevent after DNA is unraveled?

They prevent bonds from reforming.

How do DNA topoisomerases relieve tension from DNA twisting during replication?

They produce a nick in the backbone that releases tension and then reseal it.

What protein keeps DNA polymerase from falling off the DNA strand?

The sliding clamp.

What is the function of the clamp loader?

It assembles the sliding clamp.

What enzyme adds repetitive sequences to the lagging strand of DNA using its own RNA template?

Telomerase.

How does telomere length vary?

It varies by cell type and age.

What type of DNA damage involves the removal of a purine base from nucleotides?

Depurination.

What is deamination in the context of DNA damage?

It is the spontaneous loss of an amino group.

What type of DNA damage is promoted by UV radiation?

Pyrimidine-pyrimidine dimers, such as thymine dimers.

What are the general steps in a DNA repair pathway?

1. Damage DNA is recognized by nucleases. 2. Repair DNA polymerase fills the gap. 3. The nick in the backbone is sealed by ligase.

What repair mechanism specifically corrects mismatched base pairs?

Mismatch repair.

What are the two main pathways for repairing double-strand DNA damage?

Nonhomologous end joining (risky) and homologous recombination (perfect, uses an undamaged homologous double helix as a template).

Why can either DNA strand serve as a template for new DNA replication?

Because each DNA strand is complementary.

Describe semiconservative DNA replication.

It results in a DNA molecule with one old strand and one new strand.

What proteins begin DNA synthesis by binding to replication origins?

Initiator proteins.

Why are A-T rich regions often found at replication origins?

A-T base pairs have fewer hydrogen bonds, making them easier to separate during initiation.

What are the Y-shaped junctions formed during DNA replication?

Replication forks.

Is DNA replication unidirectional or bidirectional?

Bidirectional.

What enzyme catalyzes the addition of nucleotides to the 3' end of a growing DNA strand?

DNA Polymerase.

Where does the energy for DNA polymerization come from?

From the hydrolysis of phosphate bonds of the incoming deoxyribonucleoside triphosphate itself.

What are the small, separate pieces of DNA synthesized discontinuously on the lagging strand?

Okazaki fragments.

Which DNA strand is synthesized continuously?

The leading strand.

How does DNA polymerase proofread during DNA synthesis?

It clips off mispaired nucleotides and tries again.

What is required to start DNA synthesis?

A primer (RNA primer).

What enzyme synthesizes an RNA primer using a DNA template?

Primase.

How do cells rapidly adjust the local structure of chromatin?

Through ATP-dependent chromatin remodeling complexes.

What do histone modifying enzymes do?

They modify the tails of histones.

What effect does acetylation of lysines have on chromatin?

It loosens chromatin, forming euchromatin.

What effect does methylation of lysine 9 in histone H3 have on chromatin?

It condenses chromatin.

What is the difference between euchromatin and heterochromatin regarding gene expression?

Euchromatin is readily expressed, while heterochromatin is condensed and silent.

What is X-inactivation?

It is the process where one of the two X chromosomes in females is inactivated.

What is the function of the centromere during mitosis?

It allows duplicated chromosomes to bind and separate during M phase by providing an attachment point for the mitotic spindle.

What is the primary function of the nucleolus?

It makes RNA which combines with proteins to form ribosomes.

What components make up chromosomes?

DNA, histones, and nonhistone chromosomal proteins.

What is a nucleosome?

It is a structure that converts interphase DNA into chromatin, reducing its length.

What proteins make up the individual nucleosome core?

It consists of 8 histone proteins (two molecules each of H2A, H2B, H3, H4) with a segment of double-stranded DNA wrapped around them.

What is a histone octamer?

It is the complex of eight histone proteins around which DNA is wrapped in a nucleosome core.

Why are histones positively charged?

Their positive charge (due to lysine and arginine) helps them bind to the negatively charged sugar-phosphate backbone of DNA.

What are histone tails and what is their significance?

They are long N-terminal extensions from the nucleosome core that are subjected to reversible, covalent chemical modifications.

What is the role of the linker histone H1?

It helps pull adjacent nucleosomes together in a repeating array, contributing to further chromatin packing.

What do nonhistone chromosomal proteins (NHCP) do to chromatin?

They pull chromatin into loops, which are further condensed to form chromosomes.

Why are chromosomes named 'chromosomes,' and what are they composed of?

They are named 'chromosomes' (chrom=color) due to their staining properties, and they contain both DNA and proteins (histones).

Describe the basic structure of DNA.

DNA is a double helix consisting of two complementary chains of nucleotide subunits (A, T, C, G).

How are the two strands of DNA held together?

By hydrogen bonds in the base portion of the nucleotides.

What are the main chemical components of a DNA strand?

A sugar-phosphate backbone (linked by phosphodiester bonds) and nitrogenous bases (A, T, G, C).

How are the two DNA strands oriented relative to each other?

They are antiparallel.

What type of bond links the 5' end of one sugar to the 3' end of the next in a DNA strand?

Phosphodiester bonds.

What type of pairing occurs between purines and pyrimidines in DNA?

They form complementary base pairs.

Approximately how many base pairs are there per helical turn of DNA?

10 base pairs.

How many chromosomes do human cells typically carry?

46 chromosomes (23 pairs).

What are homologous chromosomes?

They are maternal and paternal copies of each chromosome.

Which chromosomes determine sex, and are they homologous in males?

X and Y chromosomes determine sex; they are nonhomologous in males (XY).

What is a karyotype?

An ordered display of all 46 chromosomes.

Define a gene.

A gene is a segment of DNA that codes for a protein.

What are the main events concerning chromosomes during interphase and mitosis in the cell cycle?

During interphase, chromosomes are duplicated. During mitosis, duplicated chromosomes are distributed and segregated to daughter nuclei.

What is a replication origin?

It is the specific site where DNA replication begins.

What is the function of telomeres?

They are protective caps made of repeated nucleotide sequences that protect the ends of chromosomes.