AP Bio Unit 4

Ap Bio DNA Replication, Cell Cycle, Mitosis, and Cancer

DNA:

• Double Helix

• Twisted Ladder

DNA Sides:

• Backbone

• Alternating sugars and phosphates

DNA Rungs:

• N-bases

• Purine & Pyrimidine

• A & T - 2 H Bongs

• C & G - 3 H Bonds

DNA Diameter:

• 2 nm

• 1 Turn = 3.4 nm

• 10 nucleotides/turn

• Vertical distance between bases = .34 nm

Anti-parallel Strands:

• One strand is oriented 5’ → 3’

• Other strand is oriented 3’ → 5’

• 5’ + 3’ refers to carbon # on deoxyribose

Models of Replication:

• Conservative

• Semi-conservative

• Dispersive

Conservative:

• Parent helix remains

• Replicated (new) DNA is made of completely new strands

Semi-Conservative:

• 2 parent strands separate and serve as a template

• Replicated (New) DNA is made of 1 old and 1 new strand

Dispersive:

• Parent DNA breaks up into pieces

• Replicated (new) DNA consists of pieces of old and new DNA

5’+3’ refer to:

carbon number on deoxyribose

DNA replication is:

• Semiconservative

Experiment (DNA replication)

• Meselson & Stahl Experiment

Step One of DNA Rep.

• Opening of helix

Step Two of DNA Rep.

• Priming

Step Three of DNA Rep.

Copying of Strands

Step Four of DNA Rep.

• Proofreading & Repair

DNA polymerase moves only in:

• 5’ → 3’

Leading Strand (oriented 5’ → 3’):

• Synthesized continuously

Lagging Strand (oriented 3’ → 5’):

• Synthesized in short segments called Okazaki fragments → 100 - 200 nucleotides

• Fragments joined by DNA Ligase to make one strand

DNA Polymerase:

• Proofreads & fixes mistakes during replication

Mismatch Repair

• Enzymes replace nucleotides

Excision Repair

• Damaged DNA is cut out & replaced

Gaps are left at 5’ end after replication when:

• Primer is removed

Each Replication:

• DNA molecule gets shorter

Prokayotes:

• Have circular DNA → no ends to shorten

Eukaryotes:

Have Telomeres and Telomerase

Telomeres:

• End of DNA molecule has repeats of nucleotide sequences instead of genes

• Protects genes from being eroded

Telomerase

• Can divide indefinitely

• Enzyme that lengthens telomeres

• Found in fetal, stem, germ-line, cancer, and gamete cells

Gel Electrophoresis

• Separates DNA molecules based on size

DNA (Charge)

• Negatively Charged

Why is dna negatively charged?

• The phosphates that form part of the dnas backbone have a negative charge

Bands closer to the well are longer where:

bands further away are shorter

Dna moves from:

Negative to positive

G₁:

• Period of growth. Important cell structures and proteins are formed.

G₀:

• Cells go here based on:

• 1. Function of the cell

• 2. Cell Crowding

Checkpoint 1:

• In G₁

• Checks:

• 1. “Is the cell growing well enough?”

• 2. “Is it’s DNA damaged?”

• 3. “Does the cel have the resources it needs if it keeps going?”

S:

• Where DNA is replicated

G₂:

• Preparation for mitosis

• Cell Growth

• Protein synthesis

• End of Interphase

Checkpoint 2:

• In G₂

• Checks if the DNA was replicated correctly back in S phase

M (Mitosis):

• Includes Prophase, Metaphase, Anaphase, Telophase, and Cytokinesis

• The stages that a cell goes through to separate the replicated DNA into two identical sets of chromosomes to be given to 2 identical daughter cells.

Checkpoint 3:

• In Metaphase

• Makes sure that replicated chromosomes are lined up in the middle properly- all attached to the spindle fibers correctly

Interphase:

• The longest and most active phase of the cell cycle

• Includes G₁, S, and G₂, phases

• Prepares for mitosis

Prophase:

• Chromatin condenses into visible X-shaped chromosomes

• Nuclear envelope breaks down and nucleolus disappears

Metaphase:

• Chromosomes become attached to the spindle fibers and align along the middle of the cell

Anaphase:

• Chromosomes break at the centromeres and sister chromatids move to the opposite sides of the cell

Telophase:

• The individual chromosomes are now at the opposite sides of the cell and two nuclei are formed

Cytokinesis:

• The cytoplasm of a single cell divides to produce two genetically identical daughter cells

Nondisjunction:

• The failure of sister chromatids to separate correctly during cell division

Positive Regulators:

• proteins that promote progression through cell cycle checkpoints

• Includes Cyclins and Cyclin-Dependent Kinases (CDKs)

Cyclin:

• Family of proteins = act as master regulators for cell cycle

• Levels go up and down throughout cycle

• Bind to CDKs to activate them

• Broken down during the Mitotic phase (M) by a death tag (protein ubiquitin) being attached to cyclin and then entering a proteasome.

Cyclin-Dependent Kinase (CDKs):

• Enzyme protein (kinase)

• Kinases activate other proteins by phosphorylating them

• Active when bound to cyclin

• Levels remain constant in cell cycle

Cyclin-CDK Complexes (When they work together):

• Formation: A specific cyclin pairs with a specific CDK.

• Activation: This binding activates the CDK, creating a "holoenzyme".

• Phosphorylation: The complex then phosphorylates target proteins, which promotes cell cycle progression (e.g., initiating DNA synthesis or building the mitotic spindle).

• Regulation: Cyclin levels rise and fall, meaning CDK activity rises and falls, allowing the cell cycle to move from one phase to the next and ensuring checkpoints are met.

Significance of Cyclins and CDKs working together:

• Cell Cycle Control: Essential for coordinating cell growth, DNA replication, and cell division.

• Disease: Dysregulation of cyclin-CDK complexes is a hallmark of cancer, making them targets for anticancer drugs.

Negative Regulators:

• Includes p53

• Can be involved in initiating apoptosis (programmed cell death)

• Act as molecular brakes, pausing or stopping the cell cycle to ensure DNA integrity and proper chromosome alignment before division

• Frequently acting at checkpoints to prevent tumor formation

p53 (Tumor Protein 53):

• A crucial tumor suppressor that prevents cancer by controlling cell division and inducing programmed cell death (apoptosis) in cells with damaged DNA, ensuring genomic stability

• . When DNA is damaged, p53 either triggers repair or eliminates the cell; mutations in TP53 are found in over half of human cancers, allowing damaged cells to proliferate and form tumors, making it a key target for cancer therapy.
  

Frequency of cell division varies with

cell type:

• Skin cells divide frequently throughout life

• Liver cells retain ability to divide, but keep it in reserve

• Mature nerve & muscle cells generally do not divide at all after maturity

Cell communication = signals (“Go-ahead signals”)

• Chemical signals in cytoplasm give cue

• Signals usually mean proteins

– Activators

– Inhibitors

Growth factors (External Signals):

• Protein signals released by body cells that stimulate other cells to divide (local or paracrine signaling)

• Example: PDGF

Density-dependent inhibition:

• Crowded cells stop dividing

– Growth factors & nutrients

are limiting factor

– When cells touch it causes

a growth inhibiting signal to

stop cell cycle

Anchorage dependence:

• To divide cells must be attached to a substrate (Culture jar or extracellular matrix of tissue)

Cancer Cells:

• Cancer cells have escaped cell cycle controls

• Cancer cells are free of both density dependent inhibition & anchorage dependence

Cancer Overrides Checkpoints:

• Cancer cells divide excessively & invade other tissues

• Cancer cells manufacture their own growth factors

• Stimulate cell division

• Stimulate blood vessel growth

Cancer Cells Divide Indefinitely:

• Cancer cells divide indefinitely if have continual supply of nutrients

– Nearly all normal mammalian cells divide 20-50 times under culture conditions before they stop, age & die

– Cancer cells may be “immortal”

• HeLa cells from a tumor removed from a woman (Henrietta Lacks) in 1951 are still reproducing in culture

DNA Damage: p53:

• When there is DNA damage, an important protein called p53 inhibits the CDK-cyclin complex, stopping the progression of the cell cycle.

• Stalling the cell cycle allows the DNA to be repaired. If the damage cannot be repaired, p53 can initiate apoptosis.

The Fate of Cells:

• Option #1: Cells undergo mitosis and divide in response to specific molecular signals, typically growth factors.

• Option #2: Cells receive signals to stop dividing in order to specialize in structure and function, a process called differentiation. Once differentiated, some cells may divide again under certain conditions.

• Option #3: Cells receive signals to undergo programmed cell death, called apoptosis, a process that eliminates unnecessary cells during development and removes unhealthy or damaged cells in a mature organism.

The Cause of Cancer:

• Normal growth and tissue maintenance depend on a balance between signals that promote and inhibit cell division.

• Two types of genes code for proteins that control and regulate the cell cycle:

– Proto-oncogenes: code for proteins which promote the cell cycle in various ways.

– Tumor suppressor genes code for proteins which inhibit the cell cycle and promote apoptosis invarious ways.

• Mutations in either of these genes can lead to uncontrolled cell division and tumor formation.

• Mutations in proto-oncogenes cause them to become oncogenes, which create proteins that overstimulate the cell cycle. Analogous to “putting the foot on the gas.”

– EX: a mutation in a gene that codes for a CDK protein could cause it to become hyperactive and make cells divide more

rapidly

• Mutations in tumor suppressor genes produce proteins that no longer inhibit the cell cycle.

Analogous to “taking the foot off the brake.”

– EX: a mutation in the gene that codes for p53 could cause it to stop inhibiting cells from dividing that are not supposed to divide.

(p53 gene mutations are involved in half of human cancers)

• Both types of mutations lead to uncontrolled cell division