BIO EXAM 3 1510: Final

What is an exception to the Central Dogma?

  HIV is a virus with an RNA genome.  When HIV infects cells, the RNA is reverse copied into DNA and then the normal flow of genetic information occurs.  This requires a unique enzyme called Reverse Transcriptase

Gene

Segment of DNA that directs the production of a protein or RNA. Unit of heredity.

Structural RNAs

RNAs that are not translated into protein and include tRNAs, rRNAs, SRP RNA,

Nucleosomes

2 loops of DNA around 8 histone proteins (2H2A, 2H2B, 2H3 2H4), Histone H1 is the linker histone between nucleosomes, The histone proteins within the nucleosome all have amino-terminal tails that extend out beyond the two loops of DNA that make up a nucleosome

Heterochromatin

highly packaged and not available for transcription, Increased H1 is found in heterochromatin, methylation is asscociated

Euchromatin

Loosely packaged and available for transcription, acetylation of histones is associated

Why are histones rich in basic (positively charged) amino acids, and how do modifications alter DNA packaging?

• Why basic: DNA is highly negatively charged (phosphate backbone). Histones' positive charge (from Lys, Arg) allows tight electrostatic binding to DNA.

• Effect of modifications: Acetylation adds acetyl groups to lysine side chains, neutralizing their positive charge, loosening histone-DNA interaction → decreases packing → increases transcription access.

Why is the G1/S checkpoint particularly crucial in cell cycle regulation?

It's the "point of no return" – once a cell passes this checkpoint and commits to DNA replication (S phase), it is biologically costly to stop. Cells with incomplete or abnormal DNA after S phase usually undergo apoptosis (programmed cell death).

What happens during G1 phase of the cell cycle?

• Function: Cell growth, organelle duplication, protein synthesis, preparation for DNA replication.

• Key Checkpoint: G1/S checkpoint (Restriction point) – checks for DNA damage, cell size, nutrients, growth signals.

What happens during S phase?

• Function: DNA replication – entire genome is duplicated to produce sister chromatids.

• Regulation: Once entered, cell is committed to complete mitosis. DNA damage checkpoints operate during S phase.

What happens during G2 phase?

• Function: Final growth and preparation for mitosis – synthesizes proteins needed for chromosome segregation (e.g., tubulin for spindle).

• Key Checkpoint: G2/M checkpoint – checks for DNA replication completion and any remaining DNA damage

M Phase (Mitosis)

Function: Cell division

• Subphases: Prophase, Prometaphase, Metaphase, Anaphase, Telophase.

• Key Checkpoint: Spindle assembly checkpoint (at metaphase) – ensures all chromosomes are attached to spindle fibers before separation.

Why must cyclin-dependent kinases (CDKs) bind to cyclins to function?

CDKs are inactive alone; binding to a specific cyclin induces a conformational change that activates the kinase. Cyclins act as regulatory subunits that control CDK activity and substrate specificity.

How does the Rb protein control the G1/S checkpoint, and what happens when it's phosphorylated?

Rb binds and inhibits E2F. Phosphorylation of Rb releases E2F to activate S-phase genes.

Why is pRb considered a tumor suppressor?

It inhibits cell-cycle progression by sequestering E2F. Loss of Rb function removes this inhibition, allowing unchecked division

Major Groove v. Minor Groove

• Major Groove: Wider/deeper. High information content – exposes base-pair edges for sequence-specific recognition by most transcription factors.

• Minor Groove: Narrower/shallower. Lower information content – often bound by proteins for non-sequence-specific interactions (e.g., histones)

Difference between the structure of RNA and DNA?

1. Sugar: DNA = deoxyribose (2' H); RNA = ribose (2' OH).

2. Base: DNA uses thymine; RNA uses uracil.

3. Strandedness: DNA is usually double-stranded; RNA is usually single-stranded but can fold.

4. Stability: DNA is chemically more stable; RNA is less stable due to 2'-OH.

What did the Meselson-Stahl experiment prove, and what was the key method?

Proved DNA replication is semi-conservative.
Method: Grew E. coli in ¹⁵N-heavy medium, switched to ¹⁴N-light medium, then tracked DNA density over generations via density-gradient centrifugation.
Result: After one generation, all DNA was intermediate density (ruled out conservative replication). After two generations, ½ intermediate, ½ light (ruled out dispersive), confirming semi-conservative model.

3’-5’ exonuclease activity is proofreading activity to make sure the correct nucleotide is incorporated

5’-3 exonuclease activity is for gap filling between Okazaki fragments and for DNA post-replication repair

What is an origin of replication?

A specific DNA sequence where the process of DNA replication begins. Crucial site where DNA replication is initiated, acting as the starting point for the assembly of the necessary replication machinery. 

In E. coli, what is the origin of replication, and what protein initiates DNA replication there?

• Origin: oriC

• Initiator Protein: DnaA binds to the 9-mer repeats in the Major groove at oriC, causing DNA bending and strand separation at the 13-mer AT-rich region, which opens the helix for replication machinery.

What is the primary function of DNA Pol I in E. coli, and what unique activity does it have?

Functions in RNA primer removal and gap filling during Okazaki fragments. Has 5’→3’ exonuclease activity to remove RNA primers ahead of synthesis (nick translation). Also has 3’→5’ proofreading.

What is the primary function of DNA Pol III in E. coli, and what are its key features?

The main replicative polymerase in E. coli, has 3’→5’ exonuclease proofreading and synthesizes both leading and lagging strands. It cannot initiate synthesis (requires RNA primer).

Function of topoisomerase and gyrase

Relieves torsional strain of overwinding

What is the origin called in Eukaryotes?

ORC in humand and ARS in yeat

What is the main function of DNA Pol α in eukaryotes?

Makes RNA primers and has no proofreading ability.

What is the primary role of DNA Pol Epsilon, and what distinguishes it?

The main leading strand polymerase in eukaryotes. 3’→5’ exonuclease proofreading

What is the primary role of DNA Polymerase β in eukaryotes, and what key repair pathway does it function in?

Main polymerase for base excision repair (BER). Fill gaps between the Okazaki fragments. removes the RNA Primer on the next Okazaki fragment using a 5’-3 exonuclease activity

What is the primary role of DNA Pol δ, and what is its key feature?

The main polymerase for lagging strand synthesis (Okazaki fragments). 3’→5’ exonuclease proofreading.