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CHAPTER 3 AND 4 - Coggle Diagram

- - - - DEFINITION: unequal sharing of electrons, Oxygen is more electronegative than Hydrogen
      - EXAMPLE: Oxygen δ–, Hydrogens δ+
    - - DEFINITION: Weak attraction between δ+ H and δ– atom (O or N)
      - EXAMPLE: H-bonds between adjacent water molecules
    - - COHESION
        
        EXAMPLE: water transport in plants
        
        DEFINITION: water molecules stick to each other
      - ADHESION
        
        DEFINITION: water molecules stick to other surfaces
        
        EXAMPLE: water clings to xylem walls
      - SURFACE TENSION
        
        DEFINITION: hard to break the surface of water
        
        EXAMPLE: water strider walking on water
  - - - DEFINITION: water sticks to itself and other surfaces
      - EXAMPLES:
        
        water droplets bead up (cohesion)
        
        capillary action in plants (adhesion)
        
        bugs on water (surface tension)
    - - SPECIFIC HEAT
        
        DEFINITION: water resists temperature change
        
        EXAMPLE: oceans moderate coastal climate
      - HIGH HEAT OF VAPORIZATION
        
        DEFINITION: heat requires to turn liquid into gas
        
        EXAMPLE: evaporation cools skin
      - EVAPORATIVE COOLING
        
        DEFINITION: high- energy molecules leave, cooling the surface
        
        EXAMPLES: sweating in humans, panting in dogs
    - - DEFINITION: ice less dense than liquid because H-bonds form from lattice
      - EXAMPLES: ice floats on pond
    - - DEFINITION: water dissolves many substances due to polarity
      - EXAMPLES:
        
        Hydrophilic: salt dissolves in water
        
        Hydrophobic: oil does not dissolve in water
  - - - DEFINITION: H₂O ⇌ H⁺ + OH⁻
      - EXAMPLE: Pure water is neutral (pH 7)
    - - DEFINITION: Pure water is neutral (pH 7)
      - EXAMPLE: Stomach acid ~2; blood ~7.4
    - - DEFINITION: Stomach acid ~2; blood ~7.4
      - EXAMPLE: HCl in stomach
    - - DEFINITION: Reduce H⁺, increase OH⁻
      - EXAMPLE: NaOH in soap
    - - DEFINITION: Resist pH change by donating/accepting H⁺
      - EXAMPLE: Carbonic acid–bicarbonate buffer in blood
  - - - DEFINITION: homogeneous mixture of subtle + solvent
      - EXAMPLE: salt water
    - - DEFINITION: Substance that dissolves another
      - EXAMPLE: Water in tea
    - - DEFINITION: Substance being dissolved
      - EXAMPLE: Sugar in coffee
    - - DEFINITION: 6.022 × 10²³ molecules (Avogadro’s number)
      - EXAMPLE: 1 mole of H₂O = 18 g
    - - DEFINITION: 1 mole of H₂O = 18 g
      - EXAMPLE:1 M NaCl = 58 g of NaCl in 1 L of water
  - - - DEFINITION: Water moves through plants by cohesion, adhesion, and transpiration.
      - EXAMPLE: Water rises in xylem of tall trees
    - - DEFINITION: Water cools organisms through evaporation
      - EXAMPLE: Humans sweat to release heat.
    - - DEFINITION: Water moderates climate by absorbing/releasing heat slowly.
      - EXAMPLE: Oceans keep coastal areas mild.
- - - - • different covalent arrangement.
      - • example: Pentane vs 2-methyl butane (both C₅H₁₂).
    - - • different around double bond.
      - • double bond = flat, not tetrahedral.
      - • cis = atoms on same side.
      - • trans = atoms on opposite sides.
    - - • mirror images.
      - • left (L) and right (D) versions.
      - • not superimposable.
      - • important in biology - some forms are active, others not.
  - - - • alcohols.
      - • polar.
      - • forms hydrogen bonds.
      - • dissolves in water.
    - - • aldehydes (end of skeleton).
      - • ketones (inside skeleton).
      - • found in sugars.
    - - • acts as an acid.
      - • donates H⁺.
      - • found in amino acids, fatty acids.
    - - • acts as a base.
      - • picks up H⁺.
      - • found in amino acids.
    - - • adds negative charge.
      - • transfers energy.
      - • found in ATP, DNA, RNA.
    - - • nonpolar.
      - • affects gene expression.
      - • can change shape/function of hormones.
- - - - SOLID (molecules vibrate in place → Example: ice)
      - LIQUID
      - GAS (molecules move freely, fast → Example: steam)
  - - - DEFINITION: Average kinetic energy of molecules
      - EXAMPLE: Human body temp = 37°C
    - - DEFINITION: Total energy of molecular motion (depends on temp & mass)
      - EXAMPLE: Pot of water has more heat than a cup at same temp
  - - - Anabolic / Endergonic : build, store energy Example: glycogen synthesis
      - Anabolic / Endergonic : build, store energy Example: glycogen synthesis
  - - - carbohydrates
      - lipids
      - proteins
      - nucleic acid
  - - - single unit/ Example: glucose
    - - chain of monomers/ Example: starch
    - - DEFINITION: Removes H + OH → forms H₂O, builds polymer
      - EXAMPLE: glucose + glucose → maltose + H₂O
    - - DEFINITION: Adds H + OH → breaks polymer into monomers
      - EXAMPLE: sucrose + H₂O → glucose + fructose
  - - - • DEFINITION: glycerol + 3 fatty acids
      - • FUNCTION: energy storage, insulation
      - • EXAMPLE: animal fat
    - - • FUNCTION: hormones, stability
        • EXAMPLE: testosterone, estrogen
  - - - • SUGAR: deoxyribose (DNA) or ribose (RNA)
        • Phosphate group
        • NITROGEN BASE: A, T, G, C (DNA); A, U, G, C (RNA)
    - - • Double helix, sugar-phosphate backbone / Double helix, sugar-phosphate backbone
    - - single strand - FUNCTION: protein synthesis - EXAMPLE: mRNA, tRNA
  - - - • Amino group (–NH₂)
      - • Carboxyl group (–COOH)
      - • R-group (variable)
    - - • Primary = amino acid sequence
      - • Secondary = alpha helix / beta sheet
      - • Tertiary = overall folding
      - • Quaternary = multiple subunits
    - - • DEFINITION: Loss of protein shape from heat or pH (cooked egg white)
  - - - • ACTIVE SITE: substrate binding site
      - • SPECIFICITY = one enzyme per substrate
      - • REACTION TYPES
        
        • synthesis: build molecules
        
        • decomposition: break molecules
      - PANCREATIC ENZYMES
        
        • AMYLASE- carbs
        
        • PROTEASE/PEPTIDASE - proteins - amino acids
        
        • NUCLEASE - nucleic acids - nucleotides
        
        • LIPASE - LIPIDS - glycerol + fatty acids
  - - - BENEDICT'S REAGENT
        
        • Tests: simple sugars
        
        • Light blue → orange (must heat)
      - BLUE LITMUS
        
        • Tests: acids
        
        • Purple-blue → pink
      - IODINE
        
        • Tests: starch
        
        • Orange-brown → purple-black
      - TEST STRIPS
        
        • Multi-compound detection
        
        • Example: urine analysis
  - - - WATER BATH
        
        • Tank of heated water with thermostat
        
        • Strength: stable heat
        
        • Weakness: risk of contamination
      - INCUBATOR
        
        • (oven) chamber heats air around samples
        
        • Strength: no risk
        
        • Weakness: temp fluctuates when door opens
- - - - • double helix (twisted ladder)
      - • backbone: deoxyribose + phosphate
      - • rungs: nitrogen bases (A, T, C, G)
      - • base pairing: A–T, C–G
    - - nucleotides = sugar + phosphate + base
        
        • examples: Human genome (~22,000 genes), chromosome 1
    - - • CHROMATIN: uncoiled DNA + proteins
      - • CHROMOSOMES: condensed DNA (visible during cell division)
      - • HOMOLOGOUS CHROMSOMES: similar pair from each parent
      - • SISTER CHROMATIDS: identical copies of replicated chromosome
      - • CENTROMERE: holds sister chromatids together
      - • KINETOCHORE: attachment point for spindle fibers
  - - - • Differences from DNA:
      - • Sugar: ribose (not deoxyribose)
      - • Bases: A, U, C, G (Uracil replaces Thymine)
      - • Single-stranded, shorter than DNA
      - TYPES AND EXAMPLES
        
        • mRNA: messenger, carries info from nucleus - ribosome
        
        • tRNA: transfer, brings amino acids to ribosome
        
        • EXAMPLE: amino acetyl tRNA synthase matches tRNA to amino acid
        
        • rRNA: structural component of ribosome
  - - - **TRANSCRIPTION**: DNA → mRNA
      - **TRANSLATION**: mRNA → Protein
  - - - • INTERPHASE: cell grows, functions, replicates DNA
        
        • G1: growth & organelles
        
        • S PHASE: DNA replication
        
        • G2: growth & prep for mitosis
        
        • MITOSIS (KARYOKINESIS) : one nucleus → two identical nuclei
      - • PROPHASE: chromatin - chromosomes, nuclear membrane breaks, centrioles move
      - • METAPHASE: chromosomes line up at equator, spindle fibers attach
      - • ANAPHASE: sister chromatids separate
      - • TELOPHASE: chromosomes - chromatin, nuclear membranes reform (Plant cell example: cell plate forms)
      - • CYTOKINESIS: division of cytoplasm (Animal: cleavage furrow) (Plant: cell plate)
  - - - STEPS
        
        • Helicase: unwinds DNA
        
        • DNA polymerase: adds complementary bases (5’ → 3’)
        
        • DNA ligase: joins Okazaki fragments (lagging strand)
      - STRANDS
        
        • Leading strand: continuous
        
        • Lagging strand: fragmented
  - - - • COMPONENTS
        
        • Pellet: dense material at bottom
        
        • Supernatant: lighter material at top
        
        • Differential centrifugation: fractioning cell parts
      - • Low speed: whole cells, nuclei
      - • Medium speed: mitochondria, lysosomes
      - • High speed: microsomes, small vesicles
      - • Very high: ribosomes, viruses
      - • Lab Tips: balance tubes, close lid, set speed/time