Biology 1A03 Test 3

Eukaryotic Cell Cycle

The series of stages that a cell goes through as it grows and divides, including interphase and mitotic phase.

Cell Division

Form of asexual reproduction for prokaryotes

Binary Fission

A type of cell division in prokaryotes where a single cell divides into two identical daughter cells.

Process of Binary Fission

Initiation: DNA attaches to plasma membrane. Elongation: As DNA replicates, the cell elongates ensuring equal DNA distribution. Division: The plasma membrane pinches inward and divides the cytoplasm, resulting in two genetically identical daughter cells.

Non- Dividing Eukaryotic Cells

Cells that are in interphase (G0) and not undergoing mitosis or meiosis. They remain metabolically active but do not replicate their DNA or divide. Examples include neurons, eye cells and muscle cells.

Importance of cell division in eukaryotes

Growth, reproduction, and repair of tissues, allowing organisms to develop, maintain, and replace cells.

Stem cells

undifferentiated cells with the potential to differentiate into various cell types, critical for growth, development, and tissue repair.

Adult stem cells

Found in fully developed organisms. Can differentiate into a restricted range of cells. Play a vital role in tissue maintenence and repair ( e.g., muscle cells)

Embryonic Stem Cells

Undifferentiated cells derived from the early stages of embryonic development, capable of giving rise to all cell types in the body, crucial for early development and regenerative medicine.

Stages of the Cell Cycle

Interphase and M Phase

Substages of Interphase

G1 ( Gap Phase ), S Phase (DNA replication), G2 (Gap Phase 2)

M Phase substages

Cell Division: Mitosis and Cytokinesis.

G1 Phase

Cell grows in size, prepares for DNA replication, duplication of organelles.

S phase

DNA replication. DNA synthesis and chromosome replication

G2 Phase

Cell continues to grow in size and begins to prepare for mitosis. Duplication of organelles to build protein machinery.

Mitosis

Division of all parts of the cell except the cytoplasm.

Stages of Mitosis

Prophase, Prometaphase, Metaphase, Anaphase, Telophase, Cytokinesis.

Prophase

Chromosomes condense and mitotic spindle forms. Marked by chromosomes becoming visible under a microscope.

Mitotic Spindle

Structure in cytosol, predominantly made of microtubules. Pulls chromosomes to opposite poles of the parent cell.

Centrosome

Compact structure that serves as a microtubule organizing centre in animal cells.

Prometaphase

Nuclear envelope dissolves, kinetochores attach to spindle.

Kinetochores

A protein structure located at the centromere of a chromosome. It serves as the attachment site for kinetochore microtubules, which help pull chromosomes apart during cell division (mitosis and meiosis). The kinetochore plays a crucial role in ensuring accurate chromosome segregation by regulating the movement of chromosomes along the mitotic spindle.

Metaphase

Chromosomes align at the metaphase plate

Anaphase

Sister Chromatids separate and move toward opposite poles (disjunctional segregation). Cell elongates.

Telophase

Nuclear envelope reforms, chromosomes decondense.

Cytokinesis

In Animals, slime molds: Cleavage furrow. In Plants: Cell wall formation.

Cleavage Furrow

Contractile ring made of actin filaments forms at the equator of the cell splitting cell.

Cell Plate Formation

Polysaccharides lay down to form cell plate which develops into new cell wall.

Regulation of the Cell Cycle

Cell cycle is controlled by cyclins and CDK’s.

Cyclins

Protein that increases throughout each stage of the cell cycle and decreases as it ends.

CDKs

Cyclin dependent kinases. Enzymes that regulate the progression of the cell cycle by phosphorylating target proteins . Only functional when bound to cyclin proteins.

Kinds of CDKs

G1/S cyclin CDK, S-Cyclin CDK, M-Cyclin CDK

G1/S cyclin CDK

Regulates DNA replication

S-cyclin CDK

Triggers DNA synthesis

M-Cyclin CDK

Promotes Mitosis

G1 DNA damage checkpoint

Prevents replication of damaged DNA

G2 DNA replication checkpoint

Ensures DNA is fully replicated before mitosis.

M-Spindle Assembly Checkpoint

Ensures chromosomes attach correctly before separation.

p53 Protein

Plays a key role in DNA damage response by halting cycle for repairs.

Significance of cell cycle regulation

Helps prevent unregulated cell division, which causes diseases like cancer.

Two Types of Microtubules in Mitotic spindle

Kinetochore and Non-Kinetochore

Kinetochore Microtubules

Attached to the kinetochore region of the chromosome. Help move chromosomes to opposite poles during anaphase.

Non-kinetochore microtubules

Interdigitating. Form cage-like network that maintains structural integrity of the cell (prevents collapse). Assist in elongating the entire cell during anaphase. NOT ATTACHED TO CHROMOSOMES. Helps activities of the cell cycle to occur without being hindered.

Importance of Gap Phases

Ensure that the parent cell is large enough in size, and has required organelles before mitosis so that daughter cell will function normally.

DNA

Macromolecule made of nucleotides that determines cell characteristics

DNA Replication

Production of a new daughter strand of DNA from a parent strand. Molecular basis of inheritance

DNA Structure

Double Helix held together by hydrogen and phosphodiester bonds.

DNA Copying Mechanism

Complementary Nitrogenous bases hydrogen-bonded to bases in parent strand.

Process of DNA Replication

DNA is unwound. Two strands are separated at the replication fork. Each strand of the old DNA serves as a template or parent strand for the synthesis of a new daughter strand. Daughter strand synthesized by attaching nucleotides to the complementary nucleotides in the parent strand.

Bond that holds bases together

Hydrogen bond.

Semiconservative Replication Model

Each DNA strand is a hybrid of old and new DNA.

Purine Bases

Adenine and Guanine. Two Carbon-Nitrogen rings

Pyrimidine Bases

Cytosine, Uracil, Thymine

Initiation (DNA Replication)

• DNA replication begins at specific sites called origins of replication.

• Helicase unwinds the DNA double helix, creating a replication fork.

• Single-strand binding proteins (SSBs) stabilize the separated DNA strands.

Elongation

• Primase adds a short RNA primer to provide a starting point.

• DNA polymerase III synthesizes new DNA by adding nucleotides in the 5' to 3' direction.

• The leading strand is synthesized continuously.

• The lagging strand is synthesized in short fragments called Okazaki fragments.

Proofreading and Error Correction

DNA polymerase has proofreading activity to correct errors.

Termination

• DNA polymerase I removes RNA primers and replaces them with DNA.

• DNA ligase seals the gaps between Okazaki fragments, forming a continuous strand.

• The result is two identical semiconservative DNA molecules (each with one old and one new strand).

Origins of replication

Prokaryotic: One Eukaryotic: multiple

Leading Strand

Synthesized continuously in 5^’ to 3^’ direction. New nucleotiddes are only added to the 3’ end.

Lagging Strand

Synthesized discontinuously in Okazaki fragments. Synthesized in 3’ to 5’ direction overall, individual fragments synthesized 5’ to 3’ (nucleotides added to 3’).

Why does prokaryotic DNA fully replicate

Because it is circular.

Telomeres

Protect chromosome ends, but shorten with each replication cycle.

Telomerease enzyme

Active in germ cells and stem cells, prevents telomere shortening by adding repeat sequences ( ex: TTAGGG in humans)

Significance of Telomerease

Telomere shortening is linked to aging and cancer.

Meselson-Stahl Experiment

• Generation 0: E. coli grown in 15N medium, DNA is fully labeled with 15N.

• Generation 1: Cells transferred to 14N medium, DNA is hybrid (15N-14N) after one division.

• Generation 2: After a second division in 14N, DNA is ½ hybrid (15N-14N) & ½ light (14N-14N) if replication is semiconservative.

Key Findings:

• Conservative replication: Would show separate 15N and 14N bands in Generation 1, which did not occur.

• Dispersive replication: Would show only hybrid DNA in Generation 2, but ½ was light, ruling this out.

• Semiconservative replication was confirmed: DNA consists of one old and one new strand in each daughter molecule.

Importance of knowing a gene sequence

To understand gene function, figure out amino acid sequrence & function of its product.

Annotation of Genome

Identifying locations of genes

Ligase

Enzyme that catalyzes of phosphodiester bonds joining new okazaki fragments in growing lagging strand.

DNA Mutations

Changes in DNA sequences. Can have positive, negative or neutral effects.

Causes of DNA Mutations

• Spontaneous Errors

• Environmental Factors (UV radiation, chemicals)

• Viruses, particularly RNA viruses, which mutate more frequently due to lack of proofreading mechanisms

Types of Mutations

1. Somatic mutations: Non-germline cells. All cells except sperm and egg cells. Cannot be inherited.

2. Germ line mutations: Sperm and Egg cells. Can be inherited.

Lederberg Experiment (1952)

Joshua & Esther Lederberg used replica plating to show that bacterial resistance to antibiotics occurs via spontaneous mutation rather than induced adaptation. They grew E. coli on a non-selective plate, then transferred colonies to a plate with antibiotics. Some bacteria survived despite never being exposed before, proving mutations happened randomly, not in response to the antibiotic.

Human Genome

All genes a human has. 3 million bps, only 2% code for proteins or regulatory RNAs.

What leads to genetic variation

Mutations and alternative alleles

What allows specialized cell function?

Different cell types express different genes.

White blood cells

Monitor infections

Red blood cells

Transport oxygen

Neutral Genetic Variation

Different Blood types

Harmful Genetic Variation

Alters protein function, leads to disease (e.g., Sickle cell anemia)

Genetic Variation that is Beneficial under certain conditions

Disease resistance mutations.

HIV Resistance (CCR5-Δ32 Mutation)

• HIV infects T cells via the CCR5 receptor.

• A 32-base pair deletion in the CCR5 gene disrupts the receptor, preventing HIV from entering cells.

• This mutation is common in European populations and may have been historically selected due to protection against bubonic plague or smallpox.

Where is the CCR5 mutation most common?

CCR5 mutation most common in europe, because of the plague and smallpox

Microbiome

Bacteria in the gut, skin and mouth. Influences digestion, immunity and health.

Microbiome DIversity

Varies by environment and diet.

2011 Microbiome Study

Found distinct microbiomes in people from USA, Japan, Europe. Same region - same microbiome, regardless of ancestry.

What influences the Microbiome the most

Diet, plant-based vs animal-based diet.

Genome vs Microbiome

Microbiome can quickly adapt to change, unlike genome.