Comprehensive Biology Study Notes (Transcribed Content, Chapters 1-4 and Key Cell Biology Concepts)

Experimental Design in Biology

Biology topic context: The Science of Life.
Experimental study design example:
- Hypothesis: Antibiotic B is more effective than Antibiotic A in current use for treating ulcers.
- Three experimental groups used to reduce variance by random assignment of a large group.
- Groups do not know who is receiving the treatment (single blind).
- Results determined by endoscopy, making it a double-blind study where the technician does not know which group the patient is in.
- Conclusion: Investigators conclude their hypothesis is supported.
Scientific studies dissemination: Placed in a scientific journal.

Matter and Basic Chemistry

Matter: anything that takes up space and has mass; existing as a solid, liquid, or gas.
Elements: basic substances; an element is a substance that cannot be broken down into another substance by ordinary chemical means.
Subatomic particles:
- Neutrons: no electrical charge, located in the nucleus.
- Protons: positive charge, located in the nucleus.
- Electrons: negative charge, outside the nucleus moving in orbitals.
Atomic structure:
- Atomic symbol: e.g., $\text{H}$ for hydrogen, $\text{Na}$ for sodium.
- Atomic Number: $Z$ , the number of protons in the element.
- Mass number: $A$ , the sum of protons and neutrons; expressed as $A = Z + N$ where $N$ is the number of neutrons.
- Electrons have about zero mass relative to protons and neutrons.
Isotopes:
- Isotopes have the same number of protons but a different number of neutrons (different mass numbers).
- Isotopes can be unstable and may decay, emitting radiation.
- Radioactive isotope behavior is essentially the same as a stable isotope of the same element.
- If an element is not a pure double (likely meaning not a pure element), then it is an isotope.

Electron Configuration and Ions

Arrangement of electrons in an atom:
- Electrons are constantly moving.
- For atoms up through atomic number 20:
- The first shell holds $2$ electrons (valence shell for the first two electrons).
- Each additional shell holds $8$ electrons.
- Atoms can lose, gain, or share electrons to achieve an outer shell of eight electrons (octet rule).
Ions:
- An ion forms when an atom loses or gains electrons.
- Positively charged ion: $\text{Cation}$ , formed when electrons are lost.
- Negatively charged ion: $\text{Anion}$ , formed when electrons are gained.

Chemical Bonds and Formulas

Molecule: a group of atoms bonded together (e.g., $\mathrm{O2},\; \mathrm{H2O},\; \mathrm{C6H{12}O6},\; \mathrm{N2}$ ).
Compound: a molecule that contains atoms of more than one element (e.g., $\mathrm{H2O},\; \mathrm{C6H{12}O6}$ ).
Types of chemical bonds:
- Ionic bond: attraction between opposite charges.
- Covalent bond: sharing electrons to complete the outer shell.
Chemical formulas:
- Reactants: molecules that participate in reactions.
- Products: molecules formed by reactions.
Acids and bases (autoprotolysis of water):
- Water splits into hydrogen ions and hydroxide ions.
- Autoprotolysis can be represented as: $\mathrm{H_2O} \rightleftharpoons \mathrm{H^+} + \mathrm{OH^-}$
pH scale:
- Range: $0-14$ .
- pH 7 is neutral.
- pH < 7 is acidic (more $\mathrm{H^+}$ than $\mathrm{OH^-}$ ).
- pH > 7 is basic (more $\mathrm{OH^-}$ than $\mathrm{H^+}$ ).
Buffers: chemical systems that resist changes in pH by taking up excess $\mathrm{H^+}$ or $\mathrm{OH^-}$ .
Blood pH: typically $7.35-7.45$ , maintained by buffers.

The Organic Molecules of Life (Chapter 3)

Lipids: have the most energy per gram among organic molecules; hydrophobic and insoluble in water.
- Functions: long-term energy storage; waterproofing (skin, hair, feathers).
- Structure: triglycerides composed of glycerol backbone and three fatty acid chains (not just two subunits).
- Fatty acids can be:
- Unsaturated: contain one or more double bonds in the carbon chain; usually liquid at room temperature.
- Saturated: no double bonds; usually solid at room temperature.
- Phospholipids: main components of the plasma membrane; have hydrophilic heads and hydrophobic tails; arrange to form a bilayer; phospholipids can flip-flop within the membrane to maintain integrity.
- Steroids: lipids with four fused rings; do not contain fatty acids; differ by functional groups; insoluble in water.
Carbohydrates: primarily used as immediate energy sources (quick energy).
- Classifications:
- Monosaccharides: single sugar molecules (e.g., $\text{Glucose},\; \text{Fructose},\; \text{Galactose},\; \text{Ribose},\; \text{Deoxyribose}$ ); easy to digest since they do not require breaking bonds (one bond to break for some disaccharides).
- Disaccharides: two monosaccharides bonded (e.g., $\text{Maltose},\; \text{Sucrose},\; \text{Lactose}$ ); require breaking only one bond.
- Polysaccharides: polymers of monosaccharides; storage or structural roles:
  - Starch (plant storage)
  - Cellulose (plant cell walls)
  - Glycogen (animal storage)
  - Chitin (exoskeletons)
Proteins:
- Monomers: amino acids; there are $20$ different amino acids.
- Functions: support, metabolism, transport, defense, regulation, motion.
- Peptide: two or more amino acids bonded.
- Peptide bond: the bond between amino acids.
- Polypeptide: a chain of amino acids.
- Amino acid sequence determines the final three-dimensional shape of a protein.
- The three-dimensional shape determines the protein's function.
Nucleic Acids:
- Primary nucleic acids: $\text{DNA}$ and $\text{RNA}$ .
- Monomers: nucleotides.
- Polymers: nucleic acids.
- Nucleotide composition: a phosphate group, a five-carbon sugar, and a nitrogen-containing base.
- Base types (typically): $\text{Adenine},\; \text{Guanine},\; \text{Cytosine},\; \text{Thymine}$ , and in RNA, $\text{Uracil}$ .

Chapter 4: Cell Theory and Cell Structure

Cell theory: every living organism is composed of one or more cells; all cells today arose from preexisting cells.
The plasma membrane: boundary between outside and inside of the cell; regulates passage in and out; composed of a phospholipid bilayer with embedded proteins; described by the Fluid Mosaic Model.
The Two Main Types of Cells:
- Prokaryotic cells: lack a membrane-bounded nucleus; generally smaller and simpler; reproduce quickly; extremely successful group.
- Eukaryotic cells: have a nucleus housing DNA; more complex, compartmentalized, with organelles.
Prokaryotes:
- Bacteria are well-known for causing disease but also have environmental roles; some are used to manufacture chemicals, food, drugs, etc.
- Prokaryotic structure example (Cytoplasm and cell envelope):
- Cytoplasm enclosed by a plasma membrane and a cell wall.
- Cell wall maintains cell shape.
- DNA is a single circular chromosome located in the nucleoid region.
- Ribosomes are the sites of protein synthesis.
Eukaryotic Cells:
- Plant and animal cells; also includes protists, fungi, and plants.
- Have a membrane-bound nucleus that houses DNA; cells are much larger and compartmentalized with organelles.
Nucleus and Associated Structures:
- Nucleus stores genetic information.
- Chromatin: diffuse DNA, protein, and some RNA.
- DNA organized into genes that specify a polypeptide.
- Nucleolus: region where ribosomal RNA (rRNA) is synthesized.
- Nuclear envelope: double membrane surrounding the nucleus.
- Ribosomes: carry out protein synthesis in the cytoplasm; present in both prokaryotes and eukaryotes; composed of two subunits and a mix of proteins and rRNA.
- Endoplasmic Reticulum (ER): physically continuous with the outer membrane of the nuclear envelope.
Endoplasmic Reticulum:
- Rough ER: studded with ribosomes; modifies proteins in the lumen.
- Smooth ER: lacks ribosomes; synthesizes lipids such as phospholipids and steroids; function varies by cell type; can produce testosterone; detoxifies drugs.
Golgi Apparatus:
- Stack of flattened membrane-bound sacs (saccules).
- Transfer station: receives vesicles from the ER; sorts and repackages proteins for destination.
Lysosomes and Vesicles:
- Lysosomes: contain digestive enzymes; digest molecules or portions of the cell.
- Vesicles: small membrane-bound packages for transport.
- Vacuoles: larger membranous sacs; can rid a cell of excess water; involved in digestion and storage.
Mitochondria:
- Found in both plant and animal cells.
- Enclosed by a double membrane.
- Break down carbohydrates to produce ATP (energy).
- Cellular respiration requires oxygen and releases carbon dioxide.
- The matrix contains its own DNA and ribosomes.
Chloroplasts:
- Use solar energy to synthesize carbohydrates via photosynthesis in plants and algae.
- Structure features: three-membrane system, double membrane enclosing stroma, and thylakoids formed from the third membrane; thylakoid membrane contains pigments that capture solar energy.
- Chloroplasts have their own DNA and ribosomes.
Cytoskeleton:
- Network of interconnected protein filaments and tubules.
- Extends from the nucleus to the plasma membrane; present only in eukaryotes.
- Maintains cell shape; motor proteins enable movement of the cell and organelles.

Chapter 11.1: Structure of DNA (brief)

Deoxyribose is a sugar used in DNA nucleotides.
The text notes that deoxyribose is a sugar (contextual introduction to DNA structure).