❤️AP Bio Unit 3 – The Cell

Key Concepts

• Cells are the fundamental unit of life and the building blocks of all living organisms
• Prokaryotic cells lack membrane-bound organelles and a true nucleus while eukaryotic cells have a true nucleus and specialized organelles
• The cell membrane is a selectively permeable barrier that controls the movement of substances in and out of the cell
  • Consists of a phospholipid bilayer with embedded proteins and carbohydrates
• Cellular respiration is the process by which cells break down organic molecules to release energy in the form of ATP
  • Occurs in the mitochondria and includes glycolysis, the Krebs cycle, and the electron transport chain
• DNA is the genetic material that carries the instructions for an organism's development and function
  • DNA replication occurs during the S phase of the cell cycle and is semi-conservative
• Mitosis is the process of cell division that produces two genetically identical daughter cells
  • Consists of prophase, metaphase, anaphase, and telophase
• Cells communicate with each other through various signaling pathways and receptors
• Microscopy techniques such as light microscopy and electron microscopy are used to visualize and study cells and their components

Cell Structure and Organelles

• The nucleus contains the cell's genetic material (DNA) and controls cellular activities
  • The nuclear envelope is a double membrane that separates the nucleus from the cytoplasm
  • Nuclear pores allow for selective transport of molecules between the nucleus and cytoplasm
• The endoplasmic reticulum (ER) is a network of membranes involved in protein and lipid synthesis and transport
  • Rough ER has ribosomes attached and is involved in protein synthesis and modification
  • Smooth ER lacks ribosomes and is involved in lipid synthesis and detoxification
• The Golgi apparatus is a stack of flattened membrane sacs that modifies, packages, and sorts proteins and lipids for transport
• Lysosomes are membrane-bound organelles that contain digestive enzymes and break down cellular waste and foreign particles
• Mitochondria are the powerhouses of the cell and the site of cellular respiration
  • Mitochondria have a double membrane structure with the inner membrane folded into cristae
• Ribosomes are the site of protein synthesis and can be found free in the cytoplasm or attached to the rough ER
• The cytoskeleton is a network of protein filaments that provides structure, support, and movement to the cell
  • Consists of microfilaments (actin), intermediate filaments, and microtubules

Cell Membrane and Transport

• The cell membrane is composed of a phospholipid bilayer with hydrophilic heads facing the aqueous environment and hydrophobic tails facing each other
• Membrane proteins are embedded in the phospholipid bilayer and serve various functions such as transport, signaling, and cell recognition
  • Integral proteins are firmly embedded in the membrane while peripheral proteins are loosely attached to the surface
• Passive transport is the movement of molecules across the membrane without the use of energy and includes simple diffusion and facilitated diffusion
  • Simple diffusion is the movement of molecules from high concentration to low concentration (down the concentration gradient)
  • Facilitated diffusion involves the use of carrier proteins to move molecules down the concentration gradient
• Active transport is the movement of molecules against the concentration gradient and requires energy in the form of ATP
  • Primary active transport directly uses ATP to move molecules (sodium-potassium pump)
  • Secondary active transport uses the concentration gradient of one molecule to move another molecule against its gradient (symport and antiport)
• Endocytosis is the process by which cells take in large molecules or particles by engulfing them with the cell membrane
  • Phagocytosis involves the engulfment of solid particles (bacteria) while pinocytosis involves the uptake of liquid droplets
• Exocytosis is the process by which cells release large molecules or particles by fusing a vesicle with the cell membrane

Energy Production in Cells

• Cellular respiration is the process by which cells break down organic molecules (glucose) to release energy in the form of ATP
• Glycolysis is the first stage of cellular respiration and occurs in the cytoplasm
  • Glucose is broken down into two molecules of pyruvate and produces a net gain of 2 ATP and 2 NADH
• The Krebs cycle (citric acid cycle) is the second stage of cellular respiration and occurs in the mitochondrial matrix
  • Pyruvate is converted to acetyl-CoA and enters the cycle, producing 2 ATP, 6 NADH, and 2 FADH2 per glucose molecule
• The electron transport chain (ETC) is the final stage of cellular respiration and occurs in the inner mitochondrial membrane
  • NADH and FADH2 donate electrons to the ETC, which are used to pump protons (H+) into the intermembrane space
  • The proton gradient is used to drive ATP synthase, producing the majority of ATP (34 ATP per glucose molecule)
• Fermentation is an anaerobic process that allows cells to produce ATP in the absence of oxygen
  • Lactic acid fermentation occurs in animal cells and regenerates NAD+ by converting pyruvate to lactate
  • Alcoholic fermentation occurs in yeast and regenerates NAD+ by converting pyruvate to ethanol and CO2
• Photosynthesis is the process by which plants and other autotrophs convert light energy into chemical energy (glucose)
  • The light-dependent reactions occur in the thylakoid membranes of chloroplasts and produce ATP and NADPH
  • The Calvin cycle (light-independent reactions) occurs in the stroma and uses ATP and NADPH to fix CO2 into glucose

DNA and Protein Synthesis

• DNA (deoxyribonucleic acid) is the genetic material that carries the instructions for an organism's development and function
  • DNA is a double helix structure composed of two antiparallel strands held together by hydrogen bonds between complementary base pairs (A-T and G-C)
• DNA replication is the process by which DNA is copied during the S phase of the cell cycle
  • Replication is semi-conservative, meaning each new DNA molecule contains one original strand and one newly synthesized strand
  • DNA polymerase is the enzyme responsible for synthesizing new DNA strands in the 5' to 3' direction
• Transcription is the process by which DNA is used as a template to produce complementary RNA (mRNA)
  • RNA polymerase binds to the promoter region of a gene and synthesizes mRNA in the 5' to 3' direction
  • In eukaryotes, mRNA undergoes post-transcriptional modifications (5' capping, 3' polyadenylation, and splicing) before leaving the nucleus
• Translation is the process by which mRNA is used as a template to synthesize proteins
  • Ribosomes read the genetic code in mRNA and translate it into a sequence of amino acids
  • tRNA (transfer RNA) molecules carry specific amino acids to the ribosome and base pair with the corresponding codons in mRNA
• The genetic code is the set of rules that determines which amino acid is added to a growing polypeptide chain based on the sequence of codons in mRNA
  • The genetic code is degenerate, meaning multiple codons can code for the same amino acid
  • Start codons (AUG) initiate translation, and stop codons (UAA, UAG, UGA) terminate translation

Cell Division and Reproduction

• The cell cycle is the series of events that take place in a cell leading to its division and duplication
  • The cell cycle consists of interphase (G1, S, and G2 phases) and mitosis (M phase)
  • Checkpoints regulate the progression of the cell cycle and ensure that conditions are suitable for cell division
• Mitosis is the process of cell division that produces two genetically identical daughter cells
  • Prophase: chromosomes condense, nuclear envelope breaks down, and spindle fibers form
  • Metaphase: chromosomes align at the equatorial plate
  • Anaphase: sister chromatids separate and move towards opposite poles
  • Telophase: nuclear envelopes reform and chromosomes decondense
  • Cytokinesis: the cytoplasm divides, resulting in two separate daughter cells
• Meiosis is a specialized form of cell division that produces haploid gametes (eggs and sperm) for sexual reproduction
  • Meiosis consists of two rounds of cell division (meiosis I and meiosis II) and results in four haploid daughter cells
  • Crossing over during prophase I allows for genetic recombination and increased genetic diversity
• Mitosis and meiosis differ in their purpose, number of cell divisions, and genetic content of the resulting cells
  • Mitosis produces genetically identical diploid cells for growth and repair, while meiosis produces genetically diverse haploid cells for sexual reproduction
• Errors in cell division can lead to genetic disorders and cancer
  • Nondisjunction during meiosis can result in aneuploid gametes and conditions such as Down syndrome (trisomy 21)
  • Uncontrolled cell division and the accumulation of mutations can lead to the development of tumors and cancer

Cell Communication

• Cell signaling is the process by which cells communicate with each other and their environment to coordinate cellular activities
• Signaling molecules (ligands) bind to specific receptors on the target cell's surface or interior
  • Hydrophobic signaling molecules (steroid hormones) can diffuse through the cell membrane and bind to intracellular receptors
  • Hydrophilic signaling molecules (peptide hormones and neurotransmitters) bind to cell surface receptors
• Signal transduction is the process by which a signal is converted into a cellular response
  • Ligand binding to a receptor triggers a series of biochemical reactions (signal transduction pathway) that amplify the signal and lead to a specific cellular response
  • Second messengers (cyclic AMP, calcium ions) are often involved in amplifying and propagating the signal within the cell
• G protein-coupled receptors (GPCRs) are a large family of cell surface receptors that transduce signals via G proteins
  • Ligand binding to a GPCR causes a conformational change that activates the associated G protein, which then activates downstream effector molecules (enzymes or ion channels)
• Receptor tyrosine kinases (RTKs) are another important class of cell surface receptors that transduce signals via phosphorylation cascades
  • Ligand binding to an RTK causes receptor dimerization and autophosphorylation, which creates binding sites for downstream signaling proteins
• Cell signaling is essential for various cellular processes, including cell growth, differentiation, migration, and apoptosis (programmed cell death)
  • Dysregulation of cell signaling pathways can lead to diseases such as cancer, diabetes, and autoimmune disorders
• Cells can communicate over short distances (paracrine signaling) or long distances (endocrine signaling)
  • Paracrine signaling involves local communication between cells via diffusible signaling molecules (growth factors)
  • Endocrine signaling involves long-distance communication via hormones released into the bloodstream by endocrine glands

Lab Techniques and Applications

• Microscopy is the use of microscopes to visualize and study cells and their components
  • Light microscopy uses visible light and lenses to magnify specimens up to ~1000x
    • Brightfield microscopy is the most common type of light microscopy and uses transmitted light to create contrast
    • Fluorescence microscopy uses fluorescent dyes or proteins (GFP) to label specific structures or molecules within cells
  • Electron microscopy uses a beam of electrons to magnify specimens up to ~1,000,000x
    • Scanning electron microscopy (SEM) produces detailed images of the surface of specimens
    • Transmission electron microscopy (TEM) produces high-resolution images of thin sections of specimens
• Cell fractionation is the process of separating cellular components based on their size, density, or biochemical properties
  • Differential centrifugation separates organelles based on their size and density by centrifuging cell lysates at increasing speeds
  • Density gradient centrifugation separates organelles based on their buoyant density using a gradient medium (sucrose or Percoll)
• Spectrophotometry is the use of light to measure the concentration of a substance in solution
  • Spectrophotometers measure the amount of light absorbed by a sample at a specific wavelength
  • Applications include measuring the concentration of proteins (Bradford assay), nucleic acids, and metabolites
• Flow cytometry is a technique used to analyze and sort cells based on their physical and chemical characteristics
  • Cells are labeled with fluorescent antibodies or dyes and passed through a laser beam one at a time
  • The scattered light and fluorescence signals are detected and used to characterize individual cells
  • Applications include cell counting, cell cycle analysis, and detecting specific cell populations (CD4+ T cells in HIV patients)
• PCR (polymerase chain reaction) is a technique used to amplify specific DNA sequences
  • PCR uses a heat-stable DNA polymerase (Taq) and specific primers to amplify a target DNA sequence through repeated cycles of denaturation, annealing, and extension
  • Applications include DNA cloning, genetic testing, and detecting infectious agents (COVID-19)
• DNA sequencing is the process of determining the precise order of nucleotides in a DNA molecule
  • Sanger sequencing uses dideoxynucleotides (ddNTPs) to terminate DNA synthesis at specific bases, producing fragments of varying lengths that are separated by capillary electrophoresis
  • Next-generation sequencing (NGS) technologies allow for high-throughput, parallel sequencing of millions of DNA fragments
  • Applications include genome sequencing, transcriptome analysis (RNA-seq), and identifying genetic variations (SNPs)