Introduction to Biology

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Biology Introduction

• Biology is the science of life (bios-life, logos-study).
• It is the study of all living organisms, acellular entities, their structure, function, growth, origin, evolution, and distribution.
• Biology relates living organisms with their environment (biotic & abiotic).

Characteristics of Life

• Living organisms must be composed of cells.
• Living organisms must be capable of growth and development.
• Living organisms must undergo metabolism.
• Living organisms must maintain homeostasis.
• Living organisms must respond to stimuli.
• Living organisms must be able to reproduce.
• Living organisms must be able to evolve and adapt.

Cell Biology - Cells

• Cells are the basic unit of life.
• The lowest level of biological structure can perform all the activities of life.
  • MNEMONICS: AMOCTOSOPCEBE (Atom-Molecule-Organelle-CELL-Tissue-Organ-System-Organism-Population-Community-Ecosystem-Biosphere-Earth).

Scientists Who Paved the Way

• Robert Hooke coined the term "cell" and was first to observe cells from an oak tree bark.
• Anton van Leeuwenhoek was the first to observe single-celled organisms( "animalcules").
• Matthias Schleiden and Theodor Schwann first recognized calls as the basic unit of life (developed the postulates of cell theory).

Cell Theory

• One or more cells make up every living entity.
• In organisms, the cell is the fundamental unit of structure and organization.
• Pre-existing cells give rise to new cells.

Prokaryotic vs Eukaryotic Cells

Prokaryotes

• Prokaryotes are unicellular and relatively simpler in structure compared to eukaryotes.
• PRO- means before, KARYON- means nut or kernel, so prokaryotes basically means "before nuclei".

Prokaryote Structures

• Cell Wall
  • Made of layers of peptidoglycan (bacteria) or pseudomurein (archaea).
  • Provides protection, maintains cellular shape, and prevents dehydration.
  • Confers structural integrity to the cell.
• Cell Membrane
  • Semi-permeable layer that functions for cellular transport while separating the cell's interior from its surroundings.
• Locomotory and Attachment Structures
  • Locomotory (motility) structures include flagella for movement (taxis).
  • Attachment structures include pilus, fimbriae, capsule, and glycocalyx.
• Cytoplasm
  • Jelly-like region within the cell where cellular components are found.
• Nucleoid Region
  • The nucleoid region contains the genetic material (DNA) of the cell.

More About Prokaryotes

• Prokaryotic cells lack a nucleus and complex organelles like mitochondria or the endoplasmic reticulum.
• Prokaryotes have membrane-bound structures that function similarly to eukaryotic organelles
• Examples of prokaryotes organelles: Anammoxosomes, Carboxysomes, Magnetosomes
• Prokaryotes are genetically and metabolically diverse than eukaryotes.
  • Estimates of prokaryotic species are in the billions or more, versus tens of millions in eukaryotes.
  • Prokaryotes have a broad species definition based on DNA-DNA similarity.
  • They have a high degree of divergence among bacterial divisions.
  • They can exchange genetic material with other organisms within the same generation, influencing phenotypes.
  • Prokaryotes are haploid, with only one copy of each gene, simplifying mutations in the lab.
  • Prokaryotic cells often contain plasmids, which are extrachromosomal DNA molecules that encode nonessential genes.

Eukaryotes

• Eukaryotes can be unicellular or multicellular.
• EU- means true or good, KARYON- means nut or kernel.
• Eukaryotic organisms are distinguished by the presence of a "true" nucleus within a membrane

Cell Components and Their Functions

Cell Membrane and Cell Transport

• The cell/plasma membrane is a semi-permeable membrane composed of a phospholipid bilayer.
  • It only allows the passive entry of certain molecules through the bilayer and other molecules through protein channels embedded within the membrane.
• The fluid mosaic model describes the structure of the plasma membrane as a mosaic of components (phospholipids, cholesterol, proteins, and carbohydrates) in which the components can flow and change position, maintaining the basic integrity of the membrane.

Cell Transport - Passive Transport

• Passive transport does not require energy (ATP).
• Substances move from an area of higher to lower concentration Passive Diffusion.
  • Diffusion through a permeable membrane follows the concentration gradient, moving the substance from high to low concentration.
• Facilitated Diffusion
  • Material moves across the plasma membrane with the assistance of transmembrane proteins down a concentration gradient
• Osmosis
  • Diffusion of water through a semipermeable membrane according to the concentration gradient of water across the membrane.

Tonicity

• Tonicity describes the amount of solute in a solution.
  • Osmolarity is the the measure of the total amount of solutes dissolved in a specific amount of solution.
• Hypotonic Solution
  • Extracellular fluid has a higher concentration of water than the cell. Water follows the concentration gradient and enters the cell. An animal cell may burst, or lyse.
• Hypertonic Solution
  • Fluid contains less water than the cell.
  • Solute draws water out of the cell, causing an animal cell to shrivel or crenate.
• Isotonic Solution
  • Extracellular fluid has the same osmolarity as the cell leading to no net movement of water.

Cell Transport - Active Transport

• Active transport uses the cell's energy, usually in the form of ATP.
• It is needed when a substance moves into the cell against its concentration gradient.

Endocytosis

• Endocytosis is active transport that moves particles (large molecules, parts of cells, and whole cells) into a cell.
• Phagocytosis
  • Large particles, such as cells, are taken in by a cell: "cell eating."
• Pinocytosis
  • Solutes needed from the extracellular fluid are taken in : "cell drinking."
• Receptor-mediated endocytosis
  • Targeted endocytosis uses binding proteins in the plasma membrane.

Exocytosis

• Exocytosis is the expulsion of material from the cell into the extracellular fluid.

Cell Cycle

• The cell cycled is an ordered series of events involving cell growth and cell division that produces new daughter cells.
• Includes mitosis, meiosis, and binary fission (bacteria).

Interphase

• Interphase is where the cell undergoes normal processes preparing for cell division
• Divided into three stages: G1 Phase (Gap 1), S Phase (Synthesis), G2 Phase (Gap 2)

G1 Phase (Gap 1)

• Little change is visible.
• Cell is active at the biochemical level accumulating the building blocks of chromosomal DNA and the associated proteins, as well as accumulating enough energy reserves to replicate each chromosome in the nucleus.

S Phase (Synthesis)

• DNA replication results in the formation of two identical copies chromosomes (sister chromatids) attached at the centromere region.

G2 Phase (Gap 2)

• The cell replenishes energy stores and synthesizes the proteins necessary for chromosome manipulation.

Mitosis

• Mitosis is the division of somatic/body cells which produces two diploid somatic cells.

Meiosis

• Meiosis is the division of the gametic cells (egg and sperm cells).
• It is divided into two phases: meiosis I and meiosis II producing four haploid daughter cells.
  • Haploid is the presence of a single set of chromosomes in an organism's cells.

Biological Molecules

• Biomolecules include chemical compounds produced by living organisms, they are the fundamental building blocks of life necessary for the proper functioning of cells and tissues.
• Biomolecules are polymers that include simpler structures known as monomers.

Biomolecules: Monomers, Functions and Structure

Enzymes

• Enzymes are biological catalysts that speed up chemical reactions without being consumed.
• Primarily proteins (some RNA molecules (ribozymes) also act as enzymes).
• Enzymes work by lowering the activation energy, making reactions more efficiently.

Substrate Binding

• Substrate Binding the substrate (the reactant molecule) binds to the enzyme's active site.
• The active site has a specific shape that matches the substrate.
• Formation of the Enzyme-Substrate Complex.
  • The enzyme undergoes a slight shape change (Induced Fit Model).
  • This stabilizes the transition state, making the reaction easier.
• Catalysis (Reaction Occurs)
  • The enzyme helps convert the substrate into the product.
  • It lowers the activation energy, causing the reaction to proceed faster.
• Product Release
  • The product is released from the enzyme.
  • The enzyme remains unchanged and is ready to catalyze another reaction.

The ATP Cycle

• Adenosine triphosphate (ATP) is the energy currency of the cell.
• ATP is made up of three components: a base, a sugar, and a phosphate chain.
• Dephosphorylation removes a phosphate group from ATP to form ADP and release energy.
• Phosphorylation adds a phosphate group to an ADP to form ATP (this requires energy)

Photosynthesis

• Photosynthesis is the process by which plants, algae, and some bacteria convert light energy into chemical energy(glucose).
• It occurs mainly in the chloroplasts of plant cells.
• The process is essential for life because provides oxygen and organic matter for other organisms.
  • General Equation of Photosynthesis: 6CO2+6H2O+lightenergy→C6H12O6+602 Reactants: Carbon dioxide (CO2), Water (H₂O), Light energy Products: Glucose (C6H12O6), Oxygen (0

Where Photosynthesis Occurs:

• Takes place in the chloroplasts of plant cells, specifically in the mesophyll of leaves.
• Chlorophyll, a green pigment, absorbs light energy to drive the reaction.
• Photosynthesis mainly happens in two stages:
  • Light-dependent reactions (thylakoid membranes): require light energy from the sun.
  • Water (H2O) splits into oxygen (O2) (byproduct). Energy carriers ATP and NADPH are produced.
    • Photon Absorption: light excites chlorophyll.
    • Water Splitting: H2O splits to replace lost electrons, releasing O2. - Electron Transport Chain (ETC): electrons pass through proteins, generating ATP and NADPH.
  • Light-independent reactions (Calvin cycle, stroma): also called dark reactions, but do not require darkness. Uses CO2 to build glucose (C6H12O6).
    • Carbon Fixation: CO2 is captured and attached to RuBP (5-carbon sugar). - Reduction Phase: ATP and NADPH help convert molecules into G3P (glyceraldehyde-3-phosphate). - Regeneration of RuBP: G3P is used to make glucose, regenerates RuBP.

Aerobic Respiration

• Aerobic respiration converts glucose and oxygen into carbon dioxide, water, and energy in the form of ATP (adenosine triphosphate).
• Occurs in the presence of oxygen, more efficient than anaerobic respiration. General Equation: C6H12O6+6O2→6CO2+6H2O+ATP. Reactants: Glucose (C6H1206) and Oxygen (02). Products: Carbon dioxide (CO2), Water (H2O), ATP

Steps of Aerobic Respiration

• Takes place in the mitochondria of eukaryotic cells.
• Glycolysis (occurs in the cytoplasm)
  • Glucose broken into two pyruvate molecules (3-carbons each). Produces small amount of ATP and NADH. Key Points: ATP Investment Phase: 2 ATPs used. ATP Payoff Phase: 4 ATPs produced (net gain of 2 ATPs). Produces 2 NADH and 2 pyruvate molecules.
• Citric Acid Cycle (Krebs Cycle, in the mitochondrial matrix)
• Pyruvate converted into acetyl-CoA enters the cycle combining with a 4-carbon molecule to form citrate (6 C). cycle produces CO2, NADH, FADH2, and a small amount of ATP. Key Points:
• For each cycle, 3 NADH, 1 FADH2, 2 CO2, and 1 ATP made. Since 2 pyruvate molecules are formed from glucose, the cycle turns twice per glucose.
• Electron Transport Chain (ETC) and Oxidative Phosphorylation (inner mitochondrial membrane): NADH and FADH2 goes to the ETC. electrons travel through releasing energy where protons (H+) create electrochemical gradient drive enzyme. ATP synthase produces ATP from ADP. Oxygen combines with water. Key Points: 1- 34 ATP is made by oxygen making the transfer.

Human Organ Systems

Homeostasis

• Homeostasis is the process by which the body maintains a stable internal environment despite external changes.
• It ensures optimal conditions for cellular functions and overall survival.
  • Key factors regulated: temperature, pH, blood pressure, glucose levels, and water balance.
• Components of Homeostasis Stimulus – environment. Receptor (Sensor) - change sends information to the control center . Control Center – information determines the response Effector shivers restore balance.

Feedback Mechanisms

• Negative Feedback:
  • Works to reverse stimulus to normal state
  • Temperature regulation:
    • Body gets to hot the sweat grands the body.
    • Body temperature decreases muscle shiver generated heat