General Biology 1 Exam 1 Study Guide Chapters 1-5

Introduction to Biology (Chapter 1)

Definition of Biology

• Biology is the scientific study of life.

The 7 Characteristics of Life

• Order: Living organisms are highly organized, coordinated structures that consist of one or more cells. Atoms make up molecules, which make up cell organelles and structures. Example: The complex symmetry of a sunflower or the cellular structure of human skin.

• Sensitivity or Response to Stimuli: Organisms respond to diverse stimuli. Movement toward a stimulus is a positive response, while movement away is a negative response. Example: Plants growing toward light (phototropism) or bacteria moving away from toxic chemicals (chemotaxis).

• Reproduction: Single-celled organisms reproduce by duplicating their DNA and dividing equally. Multicellular organisms produce specialized reproductive cells (gametes) that form new individuals. Example: A mother cat having a litter of kittens or a bacterium undergoing binary fission.

• Growth and Development: Organisms grow and develop according to specific instructions coded for by their genes. This ensures that the offspring will belong to the same species and possess characteristics similar to the parents. Example: A human infant growing into an adult or a seed developing into a tree.

• Regulation and Homeostasis: Organisms require multiple regulatory mechanisms to coordinate internal functions, respond to stimuli, and cope with environmental stresses. Homeostasis refers to the maintenance of a stable internal environment despite external changes. Example: Humans sweating to maintain a body temperature of approximately $37^{\circ}\text{C}$.

• Energy Processing: All organisms use a source of energy for their metabolic activities. Some capture energy from the sun (photosynthesis), while others use chemical energy from food (cellular respiration). Example: A butterfly drinking nectar to fuel flight.

• Evolutionary Adaptation: As a population of organisms interacts with the environment, individuals with traits best suited to their environments provide for survival and pass those traits to offspring. Example: The camouflaged fur of a desert mouse matching its environment.

The Basic Unit of Life

• The cell is the most basic unit of life. Nothing smaller than a cell is considered fully "alive" according to the shared characteristics of biological life.

Biological Hierarchy

Cellular Level

• Atoms: The fundamental units of matter.

• Molecules: Combinations of atoms.

• Organelles: Functional components within cells (e.g., mitochondria, nucleus).

• Cells: The basic unit of life.

Organismal Level

• Tissues: Groups of similar cells acting together.

• Organs: Body structures composed of several different tissues grouped together into a structural and functional unit.

• Organ Systems: Groups of organs working together (e.g., nervous system, digestive system).

• Organism: An individual living entity.

Population Level

• Population: A group of organisms of the same species living in the same place.

• Species: All populations of a particular kind of organism together, forming a distinct group whose members are similar in appearance and able to interbreed.

• Community: All the different populations of different species living together in one place.

• Ecosystem: A biological community and the physical habitat within which it lives.

• Biosphere: The entire planet Earth as a global ecosystem.

Emergent Properties

• Concept: Emergent properties arise from the interaction of components. The whole is greater than the sum of its parts; these properties are not present at the lower level of organization.

• Example: Life itself is an emergent property at the cellular level. While the organelles and chemicals within a cell are not "alive" individually, their specific interaction results in a living cell. Another example is the ability to think, which emerges from the complex interactions of neurons in the brain.

The Nature of Science

• What is Science?: Science is a systematic enterprise that builds and organizes knowledge in the form of testable explanations and predictions about the universe.

• Inductive Reasoning: The process of using specific observations to construct general scientific principles. Example: Observing that every dog you meet has fur and concluding that all dogs have fur.

• Deductive Reasoning: The process of applying general principles to predict specific results. Example: Starting with the premise that all mammals have hair, and seeing an animal with no hair, you deduce it is not a mammal.

The Scientific Method

1. Observation: Noticing a phenomenon or identifying a problem.

2. Question: Asking why or how the observed phenomenon occurs.

3. Hypothesis: Developing a suggested explanation that is testable and falsifiable.

4. Prediction: Stating what the result will be if the hypothesis is correct (often in "If… then…" format).

5. Experiment: Testing the hypothesis using controlled variables.

6. Conclusion: Analyzing data to see if it supports or rejects the hypothesis.

Charles Darwin and the Scientific Method

• Who was Darwin?: An English naturalist who proposed the theory of evolution by natural selection.

• Application: Darwin observed finches in the Galapagos Islands. He hypothesized that the different beak shapes were adaptations to different food sources. He used years of observation and data collection to test his ideas, eventually concluding that descent with modification occurs via natural selection.

Post-Darwin Evidence for Evolution

• Fossil Record: Shows transitional forms and intermediate links between groups.

• Aging Fossils: Radioactive decay allows for precise dating of fossils.

• Comparative Anatomy: Homologous structures (different functions, same evolutionary origin) and analogous structures (same function, different origin).

• Molecular Evidence: Comparison of genomes and proteins (DNA sequencing) shows degrees of relatedness.

Four Unifying Themes of Biology

1. The Cell Theory: All living organisms are made of cells; cells are the basic unit of life; all cells come from pre-existing cells. Robert Hooke first discovered cells in 1665 using a microscope to look at cork.

2. DNA (The Molecular Basis of Heredity): Information is passed from one generation to the next via Deoxyribonucleic Acid. High-fidelity replication ensures continuity.

3. Evolutionary Conservation: Some characteristics are so fundamental that they are preserved across vast stretches of time and across different species (e.g., certain metabolic pathways).

4. Evolutionary Change: Populations change over time to adapt to their environments, leading to the diversity of life observed today.

Domains and Kingdoms of Life

The Three Domains

1. Bacteria: Single-celled prokaryotes (no nucleus).

2. Archaea: Single-celled prokaryotes, often found in extreme environments; biochemically distinct from Bacteria.

3. Eukarya: Organisms with eukaryotic cells containing a membrane-bound nucleus and organelles.

The Four Kingdoms of Eukarya

1. Protista: Diverse group, mostly unicellular. Example: Amoeba.

2. Fungi: Multicellular (mostly) decomposers. Example: Mushrooms or yeast.

3. Plantae: Multicellular autotrophs (photosynthetic). Example: Oak Tree.

4. Animalia: Multicellular heterotrophs (consumers). Example: Humans.

Viruses, Ebola, and Prions

• Viruses: Considered non-living because they cannot reproduce on their own (require a host cell), do not maintain homeostasis, and lack cellular structure. However, they possess genetic material and evolve.

• Ebola: A viral hemorrhagic fever. Facts include its high mortality rate, transmission through bodily fluids, and its classification as an RNA virus.

• Prions: Infectious proteins that cause misfolding of other proteins. They are interesting because they contain no genetic material (DNA or RNA) yet can "reproduce" by inducing shape changes in normal proteins. Example: Mad Cow Disease.

The Chemistry of Life and Water (Chapters 2-4)

Basics of Matter

• Study of Chemistry: Essential because life is composed of chemicals; biology is essentially the application of chemistry in a living system.

• Matter: Anything that has mass and occupies space.

• States of Matter:

  • Solid: Fixed shape and volume (particles tightly packed).

  • Liquid: Fixed volume but takes the shape of the container.

  • Gas: No fixed volume or shape (fills container).

  • Plasma: Ionized gas with high energy.

• Mass vs. Weight: Mass is the amount of matter in an object (constant regardless of location). Weight is the force exerted on that mass by gravity (varies based on the gravitational field).

Atoms and Elements

• Atoms: The smallest unit of an element that retains the properties of that element.

• Elements: Substances consisting of only one type of atom (e.g., Carbon, Oxygen).

• Sub-atomic Particles:

  • Protons: Positively charged ($+1$), located in the nucleus, mass of approximately $1\,\text{dalton}$.

  • Neutrons: Neutral charge ($0$), located in the nucleus, mass of approximately $1\,\text{dalton}$.

  • Electrons: Negatively charged ($-1$), orbit the nucleus, negligible mass ($1/1840$ of a proton).

• Atomic Number: The number of protons in the nucleus. Defines the identity of the element.

• Atomic Mass: The sum of protons and neutrons in the nucleus. Example: Carbon-12 has $6$ protons and $6$ neutrons.

Isotopes

• Definition: Atoms of the same element that have the same number of protons but different numbers of neutrons (and thus different atomic masses).

• Use in Biology: Used for carbon dating (C-14), medical imaging, and as tracers in metabolic pathways.

Electrons and Bonding

• Electron Orbitals and Shells: Electrons inhabit energy levels (shells). The outermost shell is the valence shell.

• Valence: The capacity of an atom to bond, determined by the number of electrons needed to fill the valence shell.

• Octet Rule: Atoms are most stable when they have $8$ electrons in their valence shell (except the first shell, which holds $2$).

• Inert Atoms: Atoms with full valence shells that do not readily react. Example: Noble gases like Helium ($He$) and Neon ($Ne$).

• Electronegativity: The measure of an atom's affinity or "pull" for electrons. Oxygen and Nitrogen are highly electronegative.

Chemical Bonds

• Ionic Bond: Formed when one or more electrons are transferred from one atom to another, resulting in an attraction between oppositely charged ions (e.g., $Na^+ + Cl^- \rightarrow NaCl$).

• Covalent Bond: Formed when atoms share one or more pairs of valence electrons.

• Non-polar Covalent: Electrons are shared equally (e.g., $H-H$ or $C-H$).

• Polar Covalent: Electrons are shared unequally due to differences in electronegativity (e.g., $O-H$ in water).

• Redox Reactions: Chemical reactions involving the transfer of electrons. Oxidation is the loss of electrons; Reduction is the gain of electrons.

Water and Its Properties

• Water Molecule Structure: Two hydrogen atoms are covalently bonded (polar) to one oxygen atom. The bonds within the molecule are polar covalent bonds.

• Bonds Between Molecules: Hydrogen bonds form between the slightly positive hydrogen of one water molecule and the slightly negative oxygen of another.

• Unique Properties:

  • Cohesion: Water sticks to itself.

  • Adhesion: Water sticks to other polar surfaces.

  • High Specific Heat: Water resists changes in temperature.

  • High Heat of Vaporization: It takes a lot of energy to turn liquid water into gas, allowing for evaporative cooling.

  • Ice Density: Solid water is less dense than liquid water, so ice floats.

  • Solubility: Water is a versatile solvent for polar and ionic substances.

• Ionization of Water: Occurs when a hydrogen atom leaves its electron behind and joins another water molecule. $2H_2O \rightleftharpoons H_3O^+ + OH^-$ (often simplified to $H_2O \rightleftharpoons H^+ + OH^-$).

Acids, Bases, and pH

• Acids: Substances that dissociate in water to increase the concentration of $H^+$ ions. Example: Hydrochloric acid ($HCl$).

• Bases: Substances that combine with $H^+$ (or release $OH^-$) to decrease the concentration of $H^+$ ions. Example: Sodium Hydroxide ($NaOH$).

• pH Scale: A logarithmic scale from $0$ to $14$ measuring acidity. pH is defined as $-\log[H^+]$. A pH of $7$ is neutral; below $7$ is acidic; above $7$ is basic.

• Buffers: Substances that resist changes in pH by taking up or releasing $H^+$ ions as needed. Example: The bicarbonate buffer system in human blood.

Carbon and the Chemical Building Blocks of Life (Chapters 4-5)

Organic Chemistry Basics

• Organic Molecules: Molecules containing carbon-hydrogen bonds.

• Carbon: Ideal for building life because it has $4$ valence electrons, allowing it to form $4$ stable covalent bonds in various shapes (chains, rings, branches).

• Isomers: Molecules with the same molecular formula but different structures.

  • Structural Isomers: Differ in the actual skeleton structure.

  • Stereoisomers: Differ in how groups are attached in 3D space (cis-trans or enantiomers).

Functional Groups

Functional groups are specific groups of atoms that confer unique chemical properties to the molecules containing them:

1. Hydroxyl: $-OH$ (Polar, found in alcohols).

2. Carbonyl: $C=O$ (Found in sugars: ketones and aldehydes).

3. Carboxyl: $-COOH$ (Acidic properties).

4. Amino: $-NH_2$ (Basic properties).

5. Sulfhydryl: $-SH$ (Forms disulfide bridges in proteins).

6. Phosphate: $-PO_4^{3-}$ (Highly negative, involved in energy transfer like ATP).

7. Methyl: $-CH_3$ (Non-polar, used in gene expression regulation).

Macromolecules and Synthesis

• Monomers: Small, repeating units (building blocks).

• Polymers: Long chains of monomers linked together.

• Macromolecules:

  1. Proteins: Monomer = Amino Acids. Example: Hemoglobin.

  2. Nucleic Acids: Monomer = Nucleotides. Example: DNA.

  3. Lipids: (Not true polymers). Example: Triglycerides.

  4. Carbohydrates: Monomer = Monosaccharides. Example: Starch.

• Dehydration Synthesis: Reactions that build polymers by removing a water molecule ($H_2O$).

• Hydrolysis: Reactions that break apart polymers into monomers by adding a water molecule.

Proteins

• Functions: Enzyme catalysis, defense (antibodies), transport (hemoglobin), support (collagen), motion (actin/myosin), and regulation (hormones).

• Amino Acids: $20$ different types exist. They consist of a central carbon, an amino group ($-NH_2$), a carboxyl group ($-COOH$), a hydrogen, and a variable R-group (Side chain).

• Essential vs. Non-essential: Essential amino acids cannot be synthesized by the body and must be obtained from the diet.

• Amino Acid Classes:

  • Non-polar: Hydrophobic R-groups (e.g., methyl groups).

  • Polar: Uncharged hydrophilic R-groups (e.g., hydroxyl groups).

  • Acidic: Negatively charged R-groups.

  • Basic: Positively charged R-groups.

• Peptide Bonds: Formed between the amino group of one amino acid and the carboxyl group of another via dehydration synthesis. It is a covalent bond ($C-N$).

• Protein Structure Levels:

  • Primary: The unique sequence of amino acids.

  • Secondary: Local folding into $\alpha$-helices or $\beta$-pleated sheets due to hydrogen bonding of the polypeptide backbone.

  • Tertiary: The final 3D shape of a single polypeptide, stabilized by R-group interactions (hydrophobic interactions, ionic bonds, disulfide bridges).

  • Quaternary: The structure resulting from the assembly of multiple polypeptide subunits (e.g., Hemoglobin).

• Denaturation: The loss of native protein structure (secondary, tertiary, quaternary) due to environmental stress like heat, pH changes, or salt concentration. The protein becomes biologically inactive.

Nucleic Acids

• Function: Storage and transmission of genetic information (DNA) and protein synthesis (RNA).

• Nucleotide Structure: Consists of a 5-carbon sugar (pentose), a phosphate group, and a nitrogenous base.

• DNA vs. RNA:

  • DNA: Deoxyribose sugar, double-stranded helix, uses Thymine ($T$). Stores hereditary info.

  • RNA: Ribose sugar, single-stranded, uses Uracil ($U$) instead of Thymine. Used in protein synthesis.

• Directionality: 5' to 3' refers to the carbon numbers in the sugar. Nucleotides are added to the 3' end.

• Bonds: Phosphodiester bonds link the sugar-phosphate backbone. Hydrogen bonds link the complementary bases ($A-T$ and $G-C$).

Lipids

• Functions: Long-term energy storage, membrane structure, and signaling.

• Fats (Triacylglycerols): One glycerol molecule linked to three fatty acids. High energy density due to the high number of $C-H$ bonds.

• Saturation:

  • Saturated Fats: No double bonds between carbons; maximum number of hydrogens; solid at room temperature.

  • Unsaturated Fats: One or more double bonds ($C=C$), creating kinks in the chain; liquid at room temperature.

• Phospholipids: Two fatty acids and a phosphate group attached to glycerol. They are amphipathic (polar head, non-polar tails) and form the cell membrane bilayer.

• Steroids: Characterized by a carbon skeleton consisting of four fused rings. Cholesterol is a key component of cell membranes and a precursor to hormones.

Carbohydrates

• Functions: Short-term energy storage and structural support.

• Basic Formula: $(CH_2O)_n$. Glucose is $C_6H_{12}O_6$.

• Classification:

  • Monosaccharides: Simple sugars (e.g., Glucose, Fructose).

  • Disaccharides: Two sugars linked by a glycosidic linkage (e.g., Sucrose = Glucose + Fructose).

  • Polysaccharides: Long chains of monosaccharides.

• Key Polysaccharides:

  • Starch: Energy storage in plants (alpha-glucose chains).

  • Glycogen: Energy storage in animals (highly branched alpha-glucose).

  • Cellulose: Structural component of plant cell walls (beta-glucose chains; cannot be digested by humans).

  • Chitin: Structural component in arthropod exoskeletons and fungal cell walls.