all unjt 3
Biology 152: Cell Communication1. Signaling Molecules and Cellular Receptors1.1 Intracellular and Intercellular Signaling
Intracellular signaling: Signaling that occurs within a single cell.
Intercellular signaling: Occurs between cells in a multicellular organism, or between different single-celled organisms.
1.2 Three Stages of Cell Signaling
Reception: Chemical Signal (Ligand) binds to receptor protein on or in the target cell.
Transduction: Change in receptor's shape The binding of the ligand causes the receptor protein to change shape, initiating a sequence of changes in a series of molecules inside the cell.
Response: Transduced signal triggers a specific cellular response.
1.3 Chemical Signaling in Multicellular Organisms
Local Signaling: Communication occurs over short distances.
Autocrine signaling: The signaling cell also responds to the signaling molecule that it releases.
Direct Contact: Cell (gap) junctions - cells next to each other (touching).
Direct contact: Cell-cell recognition - ligand not soluble.
Paracrine signaling: Cell not touching (very close), ligand secreted, moving by difffusion.
Synaptic signaling: Occurs in nerve cells, where neurotransmitters are secreted into the synapse to communicate with neighboring neurons.
Long-distance signaling: Examples include hormonal (endocrine) signaling, where a cell targets a distant cell through the bloodstream.
2. Ligands and Receptors
Ligand: A signaling molecule that is complementary in shape to its receptor.
Receptor: A protein that binds to a ligand and changes shape (conformation) as a result.
Location of Receptor: Receptors may be:
Cell-surface (transmembrane) receptors: Located on the plasma membrane, bind to water soluble signal molecules.
Internal receptors: Located inside the cell (cytoplasm or nucleus). Binds to signal molecules that are hydrophobic, small, non polar molecules.
Location of the receptor tells you about the type of ligand it binds too.
2.1 Types of Cell-Surface Receptors
Ion Channel Receptors: Shape change opens a “gate” to allow ions to flow through the membrane in response to a signaling molecule.
G-Protein-Coupled Receptors (GPCRs): Binds to G protein (inside cell) and has seven alpha helices that span the membrane.
Enzyme-Linked Receptors (Receptor Tyrosine Kinases): Trigger multiple pathways at once, coordinating cellular responses. Kinases catalyze transfer of phosphate. Protein phosphatase rapidly removes phosphate groups (dephosphorylation) and usually inactivates proteins.
2.2 Example of GPCR Activity
The response to the GPCR activation is limited as the G-protein will hydrolyze GTP to GDP, leading to signal termination.
Cholera: Toxin produced by Vibrio cholerae that can disrupt G-protein signaling. Modifies a G-protein making it unable to hydrolyze GTP.
3. Signal Propagation3.1 Multistep Processes
Multistep processes allow for:
Amplification: Enhancing the signal strength.
Coordination: Ensuring multiple pathways can be activated.
Regulation: Controlling the extent and duration of the signal.
3.2 Signaling Pathway
Cascade of activation: Signal-activated receptor activates a protein that activates another molecule, continuing the cascade.
Conformation changes often result from phosphorylation or dephosphorylation events.
3.3 Protein Kinases
Protein Kinases transfer phosphate groups from ATP to other molecules, modifying their activity.
Cytoplasmic Kinases: Typically phosphorylate serine or threonine residues in target proteins.
3.4 Signaling Molecule Interaction
Large relay proteins can attach several other relay proteins simultaneously for efficient signaling.
Small, non-protein, water-soluble molecules or ions (such as Ca²⁺) are involved in signal transduction and amplification.
Ca²⁺: A widely-used second messenger that plays significant roles in muscle contraction and cell division, often found in low concentrations in the cytoplasm, stored in vesicles or entering from outside the cell.
3.5 Second Messengers
Second messengers: Small, non-protein, water-soluble molecules or ions involved in signal transduction; signal amplification.
Ca2+:Widely-used second messenger (important in muscle contraction and cell division). Used in both G-protein and receptor tyrosine kinase pathways. Typically low concentration in cytoplasm; stored in cytoplasmic vesicles or enters from outside of cell. Moves through gated channels
Cyclic AMP (cAMP): Acts as a second messenger in G-protein signaling pathways, activating cAMP-dependent kinases (A-kinases).
cGMP: Another second messenger that plays a role in various cellular processes.
Viagra (sildenafil): Works by affecting cGMP pathways. Inhibits hydrolysis of cGMP to GMP.
Inositol Phospholipids: Lipid molecules in membranes that can be converted into second messengers by phospholipase. Found in memebranes.
4. Response to the Signal
Signal transduction pathways lead to regulation of various cellular activities, including:
Gene Expression: Regulation of which genes are expressed.
Energy Metabolism: Adjusting cellular metabolism according to signaling.
Cell Growth: Coordinated by growth factors, which are ligands promoting cell growth.
Cell death
4.1 Changes in Cellular Functions
Changes in Gene Expression: Altered by signaling pathways, influencing cell functions.
Changes in Cellular Metabolism: Modified in response to signals to meet cellular needs. Ex: Epinephrine.
Cell Growth: Growth factors are ligands that promote cell growth.
4.2 Apoptosis
Apoptosis: Programmed cell death, characterized by:
Controlled process, also known as "suicide."
Fragmentation of DNA and organelles, leading to cell shrinkage and lobing ("blebbing").
Engulfment and digestion of apoptotic cells by scavenger cells.
4.3 Molecular Basis of Apoptosis
Involves a signaling transduction pathway that leads to the activation of nucleases and proteases that facilitate cell death.
5. Signal Termination
Mechanisms exist for inactivating signals to terminate the response and reset the signaling pathways. Changes in cell pathways must last only a short time. Signals produce reversible changes.
Different cells can have varied responses to the same signal due to differences in the types and quantities of receptors and internal signaling molecules present.
5.1 Clinical Applications
Example of Therapy Targeting Signal Transduction:
Lapatinib (Tykerb): An inhibitor that binds to the intracellular domain of HER2, a receptor tyrosine kinase that is permanently activated in approximately 30% of human breast cancers.
6. Signaling in Single-Celled Organisms6.1 Example with Saccharomyces cerevisiae:
Used to identify mating types:
2 mating types:
Cell type a: Secretes a factor and has receptors for the α factor.
Cell type α: Secretes α factor and has receptors for the a factor.
6.2 Quorum Sensing
Quorum Sensing: Allows bacteria to determine density of bacteria in environment. Ex: Vibrio fischeri inside of Hawaiian bobtail squid.
6.3 Autoinducers
Signaling molecules secreted by bacteria to communicate with other bacteria of the same kind.
6.4 Biofilm
Complex community of microbes that exchange chemical signals; coordinate release of virulence factors.
Cell Reproduction: Chapter 10 Origin of Cells
Cell Theory:
Established by Rudolf Virchow in the 1850s, stating: "Every cell from a cell."
Cell Division: The process leading to the production of new cells from existing cells.
Why Do Cells Divide?10.1 Cell Division
Cells divide because:
reproduction
development and growth
to replace damaged cells
DNA Copying Preceding Division: Before a cell divides, it must replicate its DNA.
Key Terms:
Genome: The complete set of genes or genetic material present in a cell.
Chromosomes: Structures within cells that contain DNA, which may exist in a condensed form (chromatin).
Chromatin: A complex of DNA and proteins that form chromosomes in eukaryotic cells.
Genes: DNA regions that code for protein.
Prokaryotes:
Have one circular chromosome.
May also possess plasmids (small, circular nonessential pieces of DNA).
Eukaryotic Cells
Multiple linear chromosomes
Somatic Cells: diploid —> 2n
All human body cells excluding gametes (sex cells).
46 chromosomes per cell
44 autosomes
2 sex chromosomes
Gametes: haploid —> n
Egg and sperm cells.
23 chromosomes per cell
22 autosomes
1 sex chromosome
Karyotype: A picture of chromosomes from 1 cell; arranged in homologous pairs.
Each duplicated chromosome comprises two identical sister chromatids.
Centromere: The location where two sister chromatids are most closely attached.
only sisters when attached
daughters chromatids when separated
The Cell Cycle10.2 The Cell Cycle
Interphase: The phase where most cells spend the majority of their life cycle. Includes three sub-phases:
G1 Phase: "First gap" period; cell grows and synthesizes proteins. Cell physically getting bigger.
S Phase: "Synthesis"; DNA is replicated.
G2 Phase: "Second gap"; cell continues to grow and prepares for division/mitosis.
Mitotic Phase: Comprises mitosis and cytokinesis.
Mitosis (Karyokinesis): The division of the nucleus and its content.
Cytokinesis: The division of the cytoplasm and its content.
Mitosis (with cytokinesis): produces 529 genetically identical daughter cells.
Meiosis: produces non identical daughter cells that have half the number of chromosomes as the parent cell.
Phases of Mitosis10.3 Phases of Mitosis
Interphase (G2): before mitosis starts: Cells grow, replenish energy, and synthesizes proteins macromolecules.
Prophase:
This is the first phase of mitosis where the nuclear envelope begins to break down, and chromosomes condense.
Spindle fibers appear and centrosomes move toward opposite poles.
Mitotic Spindle: Comprised of microtubules and associated proteins; assembles at centrioles (in animal cells).
Prometaphase:
Chromosomes continue to condense.
Kinetochores appear at the centromere and attach kinetochore microtubules.
Kinetochore: A chromosomal structure where proteins associate with specific DNA sections to form attachment points for microtubules.
Metaphase:
The mitotic spindle is fully developed, and the centrosomes are at opposite poles.
Chromosomes align at the "equatorial plate"; each sister chromatid's kinetochore is attached to a spindle fiber from opposite poles.
Anaphase:
Sister chromatids are pulled apart by the spindle fibers, becoming daughter chromosomes.
Anaphase commences when sister chromatids come apart.
Telophase and Cytokinesis:
Chromosomes reach opposite poles, starting to decondense.
The nuclear envelope reassembles, and the mitotic spindle disassembles. Cytokinesis begins, where the cytoplasm is divided.
Cytokinesis Detail:
In animal cells: A cleavage furrow forms from a contractile ring of actin microfilaments plus myosin on the cytoplasmic side.
In plant cells: Vesicles containing cell wall materials move along microtubules to the middle of the cell to form a cell plate.
Mechanism of Chromosome MovementHow Do Chromosomes Move?
Microtubules exert forces on chromosomes from opposite directions, effectively moving daughter chromosomes toward opposite poles.
2 Models:
Pac-man: microtuble disassembles at kinetochore.
Poleward Flux: microtuble disassembles at the pole.
Two models explain this mechanism:
Borisy Experiment: Utilized porcine kidney cells; microtubules were labeled with yellow dye, and a laser was used to bleach out dye in a specific region to observe movement.
What happened? they marked part of a microtuble and that mark did not move but then microtuble was still growing and shrinking at the ends.
Conclusion: microtubles are always changing, they are not fixed but are constantly building and breaking down.
Are All Cells Actively Dividing?
Are all cells in the body dividing at the same rate? No
Are all cells in the body mitotically active? No
G0 Phase
Some cells are in G0 phase:
Not actively preparing to divide
May be temporary, may be long term (neurons, cardiac muscle cells).
These cells perform normal cell functions but are not undergoing the cell cycle.
Control of the Cell Cycle10.4 Control of the Cell Cycle
Different cell types exhibit varying rates of division. Some types of cells divide often; other types of cells do not typically divide at all. Time spent in each phase of the cell cycle can vary.
Cell Cycle Control System: Triggers and coordinates cell cycle events, responding to both external and internal cues.
External Control:
Growth factors must be present for cell division.
Growth Factors: Proteins produced by cells that stimulate others to divide (e.g., Platelet-Derived Growth Factor (PDGF)). The PDGF is a hydrophilic receptor because its on the surface of the cell.
Types of External Controls
Density-Dependent Inhibition: If a spot from a mono layer of cells is removed, the cells around it will keep dividing until the space is filled, if they run out of space they will stop dividing.
Anchorage Dependence:
they have a space to attach too
most cells need to divide
Internal Checkpoints Regulation
G1 Checkpoint:
Determines if a cell proceeds to mitosis or enters G0.
Factors assessed: cell size (needs to get larger), protein reserves (needs to have enough protein), and DNA undamaged (if DNA damaged, won’t copy).
Known as the "restriction point".
G2 Checkpoint:
Assesses cell size, protein reserves, and DNA replication completeness.
M Checkpoint:
Occurs at the end of metaphase; checks if each sister chromatid is properly attached to a spindle microtubule from opposite poles.
M (spindle) checkpoint: Ensures anaphase only begins once all chromosomes are properly attached to spindle at the metaphase plate.
Regulators of the Cell Cycle
Positive Regulation:
Cyclins and Cyclin-Dependent Kinases (Cdks):
Provide go-ahead signals at the G1 and G2 checkpoints.
Cdks are only active when attached to cyclin (a protein whose concentration rises and falls within the cell during the cell cycle).
Cyclins undergo degradation at the conclusion of their activity cycle.
Negative Regulation:
Tumor Suppressor Proteins: Examples include:
Rb (Retinoblastoma Protein): Monitors cell size; when active (dephosphorylated), it binds transcription factors to block transcription.
p53: Activated in response to DNA damage; halts the cell cycle and recruits enzymes to repair DNA. Triggers apoptosis if DNA cannot be repaired.
p21: Produced when p53 levels increase; inhibits cell division by blocking Cdk/cyclin complexes.
Cancer and the Cell CycleCharacteristics of Cancer
Cancer cells:
uncontrolled cell growth
Mutations in DNA (in regions involved with cell cycle)
Cancer cells ignore cell cycle controls
Divide excessively
Do not exhibit density-dependent inhibition
Do not require added growth factors in vitro. “immortal” in vitro.
HeLa Cells:
Immortal cell line derived from Henrietta Lacks in 1951 used in various biological research. Cells are still dividing today.
Transformation to Cancer Cells
How do Cancer Cells Emerge?:
May look different from normal cells
have disrupted metabolism
cease to carry out normal cell functions
lose their attachment to neighboring cells
may lose anchorage dependence .
Tumor Types:
Benign Tumor: abnormal cells remain at original site.
Malignant Tumor: Abnormal cells invade surrounding tissue.
Metastasis:
abnormal cells spread to distinct locations and form new tumor
Cancer cells may secrete molecules that cause blood vessels to grow towards tumors.
Angiogenesis
going to need lots of nutrients and O2 to divide that why blood vessels go towards it ( more likely to metastasize so the blood vessels go towards it)
Oncogenes and Tumor Suppressor Genes
Oncogenes: cancer causing genes
Proto-oncogenes: Code for proteins that stimulate normal cell growth and division
Proto-oncogene to Oncogene Transformation:
Examples include mutations that allow cyclin-dependent kinases (Cdks) to activate without binding to cyclins, contributing to uncontrolled cell division.
Oncogene example:
ras Gene:
Encodes the Ras protein, a G protein that replays signals from growth factor receptors to protein kinases inside of cell, promoting cell cycle progression.
Notably, ras mutations are found in approximately 30% of human cancers, especially around 90% of pancreatic cancers. If mutates makes the cell divide uncontrollably.
Normal cells to cancer cells
Tumor suppressor genes: code for negative regulator proteins that prevent cell division .
Examples of Tumor Suppressor Genes:
Rb, p53, p21.
Multistep Model of Cancer Development
For a cell to become fully cancerous, approximately six genetic changes are required, including:
Appearance of an active oncogene.
Loss of functional tumor suppressor gene.
Activation of telomerase (enzyme).
Cancer Treatment Options
Radiation: A method that damages DNA to inhibit cancer cell proliferation.
Chemotherapy: A treatment involving drugs, including:
Taxol: Prevents microtubule depolymerization, disrupting cell division.
cell stops from depolymerizing so it can’t divide.
Herceptin (Trastuzumab):
type of drug that is a monoclond antibody
Her2
a receptor, herceptin stops dimerization of the receptor
Prokaryotic Cell Division10.5 Characteristics
Do Prokaryotes Perform Mitosis?:
No; no nucleus so can’t divide because they have no nucleus. Prokaryotic cells divide through binary fission.
Bacteria possess one circular chromosome, lack histones, no nucleosomes (but still have some proteins associated with DNA).
Biology 152: DNA Structure and Function Study Notes14.1 Historical Basis of Modern Understanding of DNA as Genetic Material
Key Question: How did scientists determine that DNA, and not protein, is the genetic material?
Griffith’s Experiment (1928):
Studied Streptococcus pneumoniae with two strains: "rough" (non-virulent) and "smooth" (virulent).
Conclusion:
living rough bacteria had been transformed into pathogenic S bacteria by and unknown, heritable substance from dead S cells.
Transformation: change in genotype and phenotype due to uptake of external DNA by a prokaryotic cell.
Avery's Experiment (1944):
Identified DNA as the substance that transfers generic traits.
Hershey and Chase’s Experiment (1952):
Utilized labeled bacteriophages to determine the genetic material:
Labeled DNA with phosphorus-32 ().
Labeled protein with sulfur-35 ().
Conclusion: DNA, not the protein, functions as the phases genetic material.
14.2 Structure of DNA
**Determination of DNA Structure: **
Previously established that DNA is a polymer of nucleotides.
Each DNA nucleotide consists of three parts:
Deoxyribose sugar
Phosphate group
Nitrogenous base: one of four possible bases:
Adenine (A)
Guanine (G)
Thymine (T)
Cytosine (C)
Chargaff's Rules (1947):
Observed that nucleotide composition varies between species, for example:
Humans: 30% Adenine (A)
E. coli: 26% Adenine (A)
%A=%T and %G=%C
Franklin and Wilkins (1950s):
Conducted X-ray diffraction studies on DNA.
Watson and Crick (1953):
Proposed the double helix structure of DNA.
Key Features of DNA Strands:
Complementary: A pairs with T, G pairs with C.
Antiparallel: One strand in upside down compared to the other.
Even during interphase, some regions of the eukaryotic chromosome are more tightly condensed than others:
Heterochromatin: more tightly compacted regions; genes in this region not highly expressed
Euchromatin: less compacted regions; genes in this region more likely to be expressed
14.3 DNA Replication Basics
Quotes from Watson and Crick (1953):
"It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material."
Mechanism of DNA Replication:
Referenced by Meselson and Stahl (1950s). Proved that DNA replicates semi-conservatively.
Important Features of DNA Replication in Prokaryotes:
Well-studied in E. coli, which has 4.6 million base pairs in its chromosome, replicated in approximately 42 minutes.
Growth rate of approximately 1,000 nucleotides added per second.
Replication Initiation:
Origins of replication: specific location on DNA strand where replication begins.
typically around 245 base pairs long and AT-rich.
Formation of replication forks that lead to replication bubbles, eventually merging:
Helicase: Unwinding and unzipping the DNA double helix
Single Stranded binding protein: prevents hydrogen bonds from reforming.
Topoisomerase Role:
Relieves twisting strain ahead of replication fork by breaking and rejoining DNA.
Synthesis of New DNA Strand:
primase: enzyme that catalyzes the synthesis of a new DNA strand by putting down an RNA primer (starts the new strand); new strand is built in the 5’ to 3’ direction
DNA Elongation:
DNA Polymerase: Enzymes that catalyze addition of nucleotides to growing DNA strand (it cannot start a new strand)
Nucleotides can only be added to 3’ end of DNA strand (5’—> 3’ direction)
Enzyme DNA Polymerase III adds nucleotides to primers.
14.4 DNA Replication in Prokaryotes
Coordination by Various Enzymes:
DNA Polymerases:
DNA polymerase III synthesizes the new strands:
Leading Strand: Continuously synthesized.
Lagging Strand: Synthesized in segments (Okazaki fragments).
DNA Polymerase I:
Removes RNA primer at 5’ end, replacing it with DNA by adding to adjacent 3’ end.
DNA Ligase:
Seals breaks in the sugar-phosphate backbone, connecting DNA segments together.
14.5 DNA Replication in Eukaryotes
More complex than in prokaryotes due to:
Larger and more intricate genomes,
Multiple origins of replication (humans have up to 100,000).
Presence of numerous DNA polymerases (14 known types).
Rate of replication: approximately 100 nucleotides per second.
Challenges of Eukaryotic DNA Replication:
There is a small portion of eukaryotic DNA
that cannot be replicated at the 5’ end of the strand, it cannot be copied.
Some DNA regions cannot be replicated. Specifically, telomeres which consist of repeated sequences (100 to 1,000 TTAGGG) at chromosome ends, do not contain genes and are sacrificed over successive replications to protect the coding regions.
Telomerase Enzyme:
Present in germ cells and stem cells, catalyzes the lengthening of telomeres to counteract shortening effects seen in somatic cells.
Somatic cells lack telomerase and shorten with each replication round, associated with aging.
We expect all cancer cells to express telomerease.
14.6 DNA Repair Mechanisms
High Fidelity of DNA Replication:
Generally, highly accurate with occasional mistakes.
Proofreading:
DNA polymerases check nucleotides as they are added.
Mismatch Repair:
Specialized enzymes repair incorrectly paired nucleotides during replication.
How does the repair machinery “know”
which nucleotide is correct?
in e. coli the parental strand is methylated, so the methylated strand is considered the right one.
Nucleotide Excision Repair:
Mechanism for correcting DNA damage by cutting and replacing inappropriate bases.
What happens if there is a defect in the nucleotide excision repair enzymes?
skin cancer caused easily because damaged DNA cannot be replaced.
Consequences of Repair Defects:
Xeroderma Pigmentosa:
A genetic disorder due to defects in nucleotide excision repair enzymes leading to heightened skin cancer risk due to UV sensitivity.
Mutations
Sources of Mutations:
Spontaneous: Errors occurring during DNA replication, repair, or recombination
Induced: due to environmental agents such as
Mutagen: physical and chemical agents cause mutations.
X-rays
UV Light
Ethidium bromide
Types of Point Mutations:
Base Pair Substitution: one nucleotide is substituted for another
Example: Transition effecting a single nucleotide change (e.g., from AACTG to AACCG).
Consequence: Can change one codon and affect protein outcome.
Possible outcomes:
No change in amino acid sequence (silent)
Change in one amino acid (missense)
Introduction of a stop codon (shortening the polypeptide) (nonsense)
Insertion/Deletion Mutations:
a nucleotide is added or deleted; changes reading frames of all codons “downstream”
Big impact on proteins
Example: Changing "THE CAT ATE THE RAT" to "THE ACA TAT ETH ERA T."
Types of Mutations:
Silent Mutation: No effect on protein sequence.
Missense Mutation: Results in amino acid substitution.
Nonsense Mutation: Introduces a premature stop codon.
Frameshift Mutation: Results from insertions/deletions that shift the reading frame or may introduce a stop codon inappropriately.