Honors Bio Midterm Review

The Chemical Basis of Life:

📘 1. Intro to Organic Compounds (3.1–3.3)

Ch. 3.1-3.3 (Intro to Organic C…

Carbon — The Basis of Life

• Organic molecules contain C–C or C–H bonds.

• Carbon can form 4 covalent bonds, allowing:

  • Chains

  • Branches

  • Rings

• Isomers = same formula, different structure.

• Hydrocarbons = only carbon + hydrogen.

Functional Groups

Functional groups determine chemical behavior of molecules.

Examples:

• Hydroxyl (–OH)

• Carbonyl (=O)

• Carboxyl (–COOH)

• Amino (–NH₂)

• Phosphate (–PO₄)

These groups make molecules hydrophilic and reactive.

Macromolecules, Polymers & Monomers

All living things are made of 4 major macromolecules:

1. Carbohydrates

2. Lipids

3. Proteins

4. Nucleic acids

Monomer → Polymer

• Built by dehydration reaction (water removed).

• Broken by hydrolysis (water added).

• Both processes require enzymes.

📘 2. Carbohydrates & Lipids (3.4–3.11)

Carbohydrates (C, H, O)

Functions

• Quick energy source

• Structural support in plants (cellulose)

Types

• Monosaccharides (monomers):

  • Glucose, fructose

  • 5–6 carbon atoms

• Disaccharides (dimers):

  • Sucrose = glucose + fructose

• Polysaccharides (polymers):

  • Starch (plants)

  • Glycogen (animals)

  • Cellulose (plant cell walls)

Nutrition Note

• Added sugars = “empty calories”
  → energy but no nutrients.

Lipids (C, H, O)

Functions

• Long-term energy storage

• Cell membrane structure (phospholipids)

• Hormones (steroid-based)

Structure

• Glycerol + fatty acid chains

• Nonpolar, hydrophobic

• Two major types:

  • Saturated fats (solid; animal fats)

  • Unsaturated fats (liquid; plant oils)

Important Lipids

• Triglycerides — typical fats and oils

• Phospholipids — form cell membranes

• Steroids — cholesterol, sex hormones

Health Topics

• Hydrogenation creates trans fats → major health risks.

• Anabolic steroids = synthetic testosterone → dangerous effects.

📘 3. Proteins & Nucleic Acids (3.12–3.16)

Ch. 3.12-3.16 (Proteins & Nucle…

Proteins (C, H, O, N, sometimes S)

Functions

Proteins do nearly everything:

• Enzymes

• Hormones

• Antibodies

• Transport (membrane proteins)

• Structural (collagen)

• Movement (muscle fibers)

Monomer → Amino Acids

• 20 amino acids

  • 12 made by your body

  • 8 essential (from food)

Polymer → Polypeptide

• Amino acids linked by peptide bonds (dehydration reaction).

• Sequence determines structure → determines function.

Protein Structure (4 Levels)

1. Primary — amino acid sequence

2. Secondary — coils & sheets (H-bonds)

3. Tertiary — 3D folding (R-group interactions)

4. Quaternary — multiple polypeptides together

Denaturation: protein loses its shape → loses function.

Nucleic Acids (C, H, O, N, P)

Functions

• Store genetic information (DNA)

• Transmit genetic instructions (RNA)

Monomer → Nucleotide

Each nucleotide contains:

• Sugar

• Phosphate

• Nitrogen base (A, T, C, G, U)

Polymer → DNA or RNA

• DNA: double-stranded, genetic blueprint

• RNA: single-stranded, used for protein synthesis

Your unique traits come from your unique nucleotide sequence.

The Cell:

📘 Concept 1: Cell Theory & Organelles

Cell Theory

1. All living things are made of cells.

2. Cells are the basic unit of life.

3. All cells come from other cells.

Types of Organisms

• Unicellular — made of one cell

• Multicellular — many cells that form tissues → organs → organ systems

Two Types of Cells

Prokaryotic Cells

• No nucleus

• No membrane-bound organelles

• Divide by binary fission

• Always unicellular

• Cell wall made of peptidoglycan

• Example: bacteria

Eukaryotic Cells

• Have a nucleus

• Have membrane-bound organelles

• Divide by mitosis

• Uni- or multicellular

• Cell walls only in plants (cellulose) and fungi (chitin)

• Example: animals, plants, fungi, protists

All Cells Have:

• DNA/RNA

• Cell membrane

• Ribosomes

• Cytoplasm

Organelles Overview

Organelles work together for one main purpose: MAKING PROTEINS.

CELL MEMBRANE

• Structure: phospholipid bilayer with proteins & carbs

• Job: regulates what enters/exits; maintains homeostasis

• Selectively permeable

• Uses Fluid Mosaic Model

CYTOSKELETON

• Protein fibers

• Gives shape, moves organelles

• Important for support in animal cells

CYTOPLASM

• Jelly-like, mostly water

• Holds organelles, site of chemical reactions

NUCLEUS

• Contains DNA

• Nuclear envelope with pores

• Control center of the cell

Nucleolus

• Inside nucleus

• Makes rRNA for ribosomes

RIBOSOMES

• Made of proteins + rRNA

• Location: rough ER or free-floating

• Make proteins

  • Rough ER ribosomes → proteins for export

  • Free ribosomes → proteins used inside cell

ROUGH ER

• Covered in ribosomes

• Makes & packages proteins

SMOOTH ER

• No ribosomes

• Makes lipids

• Stores calcium

GOLGI APPARATUS

• Folded membranes

• Receives vesicles from ER

• Sorts, processes, ships proteins

LYSOSOMES (Animal cells only)

• Contain enzymes

• Break down bacteria, old cell parts

• Can perform apoptosis

VACUOLES

• Store water, nutrients, waste

• Many small in animals; one large central vacuole in plants

CENTRIOLES (Animal cells only)

• Made of microtubules

• Help with cell division (spindle fibers)

CILIA & FLAGELLA

• Cilia: many short projections → movement across surface

• Flagella: few long tail-like structures → move entire cell

• Found mostly in animal cells and some bacteria

MITOCHONDRIA

• “Powerhouse of the cell”

• Site of cellular respiration

• Makes ATP

CHLOROPLAST (Plant cells only)

• Site of photosynthesis

• Contains chlorophyll

• Converts solar energy → sugar

CELL WALL (Plants, fungi, bacteria)

• Structural support

• Plant = cellulose

• Fungi = chitin

• Bacteria = peptidoglycan

⭐ 📘 Concept 2: Cell Transport

Homeostasis

• Stable internal conditions

• Maintained through cellular transport

Feedback Mechanisms

Positive Feedback (amplifies)

• Examples:

  • childbirth contractions

  • fruit ripening

Negative Feedback (stabilizes)

• Examples:

  • thermoregulation

  • blood sugar regulation

  • osmoregulation

Cell Membrane & Transport

• Membrane is selectively permeable

• Two major types of transport:

  1. Passive transport — no energy

  2. Active transport — requires energy (ATP)

Passive Transport (High → Low concentration)

1. Simple Diffusion

• Small, nonpolar molecules (O₂, CO₂)

• Move directly through membrane

2. Facilitated Diffusion

• Uses transport proteins

• For large or polar molecules (glucose, ions)

3. Osmosis

• Diffusion of water

• High water → low water

Tonicity

• Hypertonic — water moves OUT → cell shrivels

• Hypotonic — water moves IN → cell swells

• Isotonic — no net change

Active Transport (Low → High concentration)

1. Molecular Pumps

• Uses energy + protein pumps

• Moves ions (Na⁺, K⁺, Ca²⁺, Cl⁻)

2. Endocytosis (into cell)

• Phagocytosis — cell “eating” solids

• Pinocytosis — cell “drinking” liquids

3. Exocytosis

• Vesicles release materials outside the cell

• Example: nerve cells releasing neurotransmitters

⭐ 📘 Concept 3: Cell Cycle & Cancer

Cell Division Overview

• A fertilized egg divides repeatedly → many identical cells

• Through mitosis

• Differentiation → specialized cells → tissues → organs → organ systems

Stem Cells

• Embryonic — undifferentiated

• Adult — partially differentiated (bone marrow)

Cell Cycle

Repeated pattern of growth + division in eukaryotes.

3 Main Phases

1. Interphase

2. Mitosis

3. Cytokinesis

⭐ 1. INTERPHASE (G1, S, G2)

The longest phase.

G1 — Growth 1

• Cell grows

• Makes proteins

S — DNA Synthesis

• DNA replicates

• Chromosomes duplicate → sister chromatids

G2 — Growth 2

• More growth

• Prepares for division

⭐ 2. MITOSIS (PMAT)

Produces 2 identical daughter cells

Prophase

• Chromosomes condense → visible

• Nuclear membrane dissolves

• Spindle fibers form

Metaphase

• Chromosomes line up in middle

• Spindle fibers attach to centromeres

Anaphase

• Sister chromatids separate

• Move to opposite ends

Telophase

• Chromosomes decondense

• New nuclei form

• Spindle breaks down

⭐ 3. CYTOKINESIS

• Cytoplasm divides

• Animal cells: cleavage furrow

• Plant cells: cell plate

Cell Division Rates

• Different cells divide at different speeds:

  • Intestines: every 5 days

  • Skin cells: every 2 weeks

  • RBCs: every 4 months

  • Liver cells: every 1 year

Cells divide for: GROWTH + REPAIR

Regulation of the Cell Cycle

Controlled by:

• Internal signals (DNA)

• External signals (hormones, nutrients)

• Checkpoints (G1, S, G2, M)

When regulation fails → disease

⭐ Apoptosis

Programmed cell death

• Helps shape organisms (ex: webbed fingers)

• Removes damaged cells

⭐ Cancer

• Uncontrolled cell division

• Caused by loss of regulation

• Forms tumors

Types of Tumors

• Benign — contained

• Malignant — spreads; invasive

• Metastasis — cancer spreading to new tissues

Causes of Cancer

• Genetic mutations

• Carcinogens (chemicals, smoke, asbestos)

• Radiation (UV exposure)

• Viruses (HPV)

• Lifestyle factors (diet, smoking, activity level)

Energy Flow:

📘 Concept 1: Enzymes

Metabolism Basics

• Metabolism = all chemical reactions in the cell that provide energy and create key molecules.

• Chemical reactions involve breaking and forming bonds.

  • Breaking bonds → requires energy

  • Forming bonds → releases energy

• No energy is ever “lost” — it transforms (often released as heat or light).

Types of Reactions

• Catabolic reactions (exergonic)

  • Break down large molecules into smaller ones

  • Release energy

• Anabolic reactions (endergonic)

  • Build larger molecules from smaller ones

  • Require energy

Activation Energy

• Amount of energy required to start a reaction.

• Enzymes reduce this energy → making reactions faster.

Enzymes

• Proteins that act as catalysts.

• Speed up reactions by lowering activation energy.

• Bind to specific substrates at an active site (“lock and key” → induced fit).

• Not used up — reusable.

How Enzymes Work

• Can break substrates apart into products

• Or combine substrates into one product

Enzyme Specificity

• One enzyme = one substrate

• Shape of active site determines function

Denaturation

• Enzyme loses shape → loses function

• Caused by:

  • Extreme pH

  • Temperature changes

  • Ionic strength/solubility

• Some enzymes can renature, many cannot.

Factors Affecting Reaction Rate

1. Temperature ↑ → reaction rate ↑

2. pH → enzymes only work in specific pH ranges

3. Substrate concentration ↑ → faster reaction

4. Catalysts (enzymes) → speed up reaction

5. Competitive inhibitors → slow reaction by blocking active sites
   📘 Concept 2: ATP

What is ATP?

• Adenosine Triphosphate

• Main energy-carrying molecule of the cell

• Composed of:

  • Adenine (nitrogen base)

  • Ribose (sugar)

  • 3 phosphate groups (high-energy bonds)

How ATP Works

• The energy is stored in the bond between the last two phosphates.

• When this bond breaks → ATP → ADP + P + energy

ATP ↔ ADP Cycle

• ATP breaks → energy released (exothermic)

• ADP + P → ATP (requires energy; endothermic)

Chemiosmosis

• Ions move down concentration gradient

• ATP synthase adds the phosphate onto ADP

• This happens during cellular respiration in mitochondria

Where Energy Comes From

• From breaking down macromolecules:

  • Carbohydrates → 36 ATP per glucose

  • Lipids → most energy per gram (9 cal/g)

  • Proteins → rarely used for energy

📘 Concept 3: Energy Flow

Two Types of Energy Users

Producers (Autotrophs)

• Get energy from nonliving sources

• Perform photosynthesis or chemosynthesis

• Examples: plants, algae, cyanobacteria

Consumers (Heterotrophs)

• Get energy from living or once-living organisms

• Types:

  • Herbivores

  • Carnivores

  • Omnivores

  • Detritivores (decomposers)

Food Chains

• Show a single path of energy flow

• Trophic levels:

  1. Producers

  2. Primary consumers

  3. Secondary consumers

  4. Tertiary consumers

Rule of 10

• Only 10% of energy moves to the next trophic level

• 90% is “lost” as heat or used for metabolism

Food Webs

• Show many interconnected food chains

• More accurate representation of ecosystems

Trophic Pyramids

• Energy pyramid = energy available at each level

• Numbers pyramid = number of organisms

• Biomass pyramid = total organic mass

• Always get smaller toward the top

📘 Concept 4: Photosynthesis

What Is Photosynthesis?

• Process where plants convert sunlight + water + CO₂ into glucose + O₂

• Endothermic reaction

• Equation:
  6CO₂ + 6H₂O + sunlight → C₆H₁₂O₆ + 6O₂

Chloroplast Structure

• Grana/thylakoids → where light-dependent reactions occur

• Stroma → where Calvin Cycle happens

Why Plants Are Green

• Contain chlorophyll a + b and carotenoids

• Absorb all colors except green

• Green is reflected → we see plants as green

Photosynthesis Stages

1. Light-Dependent Reaction

• Location: thylakoid membrane

• Requires sunlight

• Purpose:

  • Split water

  • Release oxygen

  • Charge ATP & NADPH (electron carriers)

• Key processes:

  • Electron Transport Chain

  • Chemiosmosis

  • Photosystems absorb light

2. Light-Independent Reaction (Calvin Cycle)

• Location: stroma

• Does not require light

• Uses ATP + NADPH from light-dependent reactions

• Purpose: make glucose

Process:

1. Grab — CO₂ enters, joins with RuBP

2. Split — becomes 3-carbon molecules (PGA)

3. Leave — one G3P leaves to form glucose

4. Switch — remaining G3P regenerates RuBP

Rate of Photosynthesis Affected By:

• Light intensity

• CO₂ concentration

• Temperature

Alternate Pathways

CAM plants

• Open stomata at night, close during day

• Example: cacti, pineapples

C4 plants

• Close stomata during hottest times

• More water-efficient

• Example: corn, sugarcane

📘 Concept 5: Cellular Respiration

What Is It?

• Process that converts glucose → ATP

• Exothermic reaction

• Equation:
  C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O + ATP

Where It Happens

• In the mitochondria

• Structure:

  • Matrix → Krebs Cycle

  • Inner membrane (cristae) → ETC

STAGE 1 — Glycolysis

• Location: cytoplasm

• Anaerobic (no oxygen required)

• Splits glucose → 2 pyruvate

• Net gain: 2 ATP + 2 NADH

Decision Point: Oxygen Available?

A. If Oxygen IS Present — Aerobic Respiration

Stage 2 — Krebs Cycle (Citric Acid Cycle)

• Location: matrix

• Pyruvate → Acetyl-CoA → enters cycle

• Produces (for 2 pyruvate):

  • 8 NADH
    2 FADH₂

  • 2 ATP

  • 6 CO₂ (waste)

Stage 3 — Electron Transport Chain (ETC)

• Location: inner membrane

• Uses NADH/FADH₂ to make 34 ATP

• Oxygen = final electron acceptor

  • Combines with H⁺ → makes water

• Most ATP comes from this step!

Total ATP in Aerobic Respiration:

36–38 ATP

B. If Oxygen Is NOT Present — Anaerobic Respiration

Fermentation Types

1. Lactic Acid Fermentation

• In animals + some bacteria
  Produces lactic acid + 2 ATP

2. Alcohol Fermentation

• In yeast

• Produces alcohol + CO₂ + 2 ATP

Total ATP without oxygen: 2–4 ATP