Last Minute Review: Biology Exam

Intro

This is my desperate attempt to study for the Biology exam.

• Chapter 7 & 11: Membrane Transport and Cell Signaling
• Chapter 8: Metabolism
• Chapter 9: Cellular Respiration and Fermentation
• Chapter 10: Photosynthesis

Membrane Transport and Cell Signaling

• Overview
  • Membrane exhibits selective permeability
  • Phospholipids (amphipathic molecules)
    • Hydrophilic head
    • Hydrophobic tail
  • The fluid mosaic model
• Fluidity of membranes
  • Shift laterally (but can’t flip because of Hydrophobic tails)
  • Unsaturated (more fluid) vs saturated (most stable)
  • Cholesterol
• Membrane Proteins and Their Functions
  • Integral proteins
  • Peripheral proteins
  • Six functions of membrane proteins
    1. Transport
    2. Enzymatic activity
    3. Anchor (attachment to the cytoskeleton and extracellular matrix) (?)
    4. Cell-cell recognition
    5. Interceullar joining (?)
    6. Signal Transduction
  • Membrane faces are different from each other
• Selective Permeability
  • Hydrophobic molecules can cross easily
  • Polar molecules, such as sugars, cannot cross easily
• Transport Proteins
  • Channel proteins
    • Have a hydrophilic channel that allows passage of hydrophilic substances
  • Carrier proteins
    • Bind to molecules and change shape to shuttle them across the membrane
  • A transport protein is specific
• Tonicity
  • A is hypertonic to B, if A has a higher solute concentration than B
  • A is hypotonic to B, if A has a lower solute concentration than B
  • Plant cells want to be in a hypotonic environment, so that they will gain water (become turgid)
• Passive transport
  • Diffusion of a substance across a membrane with no energy investment
  • Substances diffuse down their concentration gradient
  • The diffusion of a substance across a biological membrane is passive transport
  • Osmosis is the diffusion of water across membranes
  • Facilitated diffusion
    • Still passive; just speed up the process
    • Examples: channel protein
• Active Transport
  • Move solutes against their concentration gradient
  • Needs energy, usually in the form of ATP
  • Example: Sodium-potassium pump
    • 3 Na+ in
    • 2 K+ out
• Cotransport
  • Active transport of a solute indirectly drives transport of other solutes
• Bulk Transport
  • Requires energy
  • Occurs by exocytosis and endocytosis
    • Exocytosis
    • Endocytosis - cell takes in molecules
      • Phagocytosis (cellular eating)
      • Pinocytosis (cellular drinking)
      • Receptor-mediated endocytosis
• Cell Signaling
  • Short-distance signaling: paracrine signaling
  • Neuron-related signaling: synaptic signaling
  • Long-distance signaling: endocrine signaling (through blood vessels)
  • Autocrine: signaling with itself
• Three Stages of Cell Signaling
  • Reception
  • Transduction
  • Response (activation)
• Reception: the Binding of a Signaling Molecule to a Receptor Protein
  • Binding between a signal molecule (ligand) and receptor is highly-specific
  • Receptors
    • G protein-coupled receptors (GPCR)
      • G proteins bind to GTP (a Canadian cousin of ATP)
      • G protein is active if and only if GTP is bound to the G protein
    • Ligand-gated ion channels
      • When a signal molecule binds to a receptor, the gate changes shape and allows specific ions to pass
• Transduction
  • Involves multiple steps
    • Can amplify a signal
  • The molecules that relay a signal are mostly proteins
  • Phosphorylation and Dephosphorylation
    • Protein kinases transfer phosphates from ATP to proteins
      • Change protein from inactive to active
    • Protein phosphatases remove the phosphates from proteins
      • Turning off the signal transduction pathway
  • Second messengers
    • Activates the series of proteins
    • Cyclic AMP and ions are common second messengers
• Response
  • Response may occur in the cytoplasm or in the nucleus
  • Transcription factor
  • QUESTION: explain in human language

Metabolism

• Catabolic vs Anabolic
  • Catabolic pathways release energy by breaking down complex molecules
  • Anabolic pathways consume energy to build complex molecules
• Exergonic vs Endergonic
  • Exergonic reactions have negative net free energy (delta G is negative)
  • Endergonic absorbs free energy (delta G is positive)
• ATP
  • Energy coupling
    • The use of exergonic process to drive an endergonic one
    • Mediated by ATP
  • ATP drives endergonic reactions by phosphorylation
  • ATP can be regenerated by an addition of phosphate group to ADP
  • Cycle of life
• Enzymes
  • An enzyme is a catalytic protein that speeds up reactions
  • Properties of enzymes
    • Activation energy is the initial energy required to start a chemical reaction; enzymes lower the activation energy
    • Enzymes do not affect the change in free energy
  • Induced fit of enzyme to the substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction
  • An enzyme’s activity can be affected by:
    • Temperature and pH
      • Each enzyme has an optimal temperature and pH
  • Cofactors
    • Non-protein enzyme helpers (recall that enzymes are proteins)
    • An organic cofactor is called a coenzyme
  • Enzyme inhibitors
    • Competitive inhibitors
      • Bind to the active site of an enzyme
    • Noncompetitive inhibitors
      • Bind to another part of an enzyme to make the active site less effective
    • Allosteric regulation (QUESTION)
    • Feedback inhibition
      • The end product of a metabolic pathway shuts down the pathway
      • Prevents waste

Cellular Respiration and Fermentation

• Overview
  • Cellular respiration is made up of both aerobic and anaerobic respiration (otherwise known as fermentation)
  • Exergonic
  • The fuel (i.e. glucose) gets oxidized, while oxygen is being reduced
  • Multi-step process:
    • glycolysis (occurs in cytoplasm)
    • pyruvate oxidation and citric acid cycle (kreb’s cycle)
    • oxidative phosphorylation (generates most of the ATP)
• Redox
  • Reduced (gain an electron)
  • Oxidized (lose an electron)
• Glycolysis
  • Breaks down glucose into two pyruvates
  • Investment phase
    • Uses 2 ATP
    • Breaks glucose into PGAL
  • Payoff phase
    • PGAL turns into pyruvate
    • Gains 4 ATP and 2 NADH (reduced NAD+)
• Citric Acid Cycle
  • Occurs in the mitochondria
  • Pyruvate oxidation
    • Take a carbon from pyruvate, attach CoA, and form Acetyl CoA
    • Produces a CO2 and a NADH
  • Kreb’s cycle
    • Acetyl CoA (2 carbon) + oxaloacetate (4 carbon) -> citrate acid (6 carbon)
    • Citrate acid -> gets oxidize a bunch of times -> malate -> oxaloacetate
    • Notice that 3 total carbons are lost in the entire cycle
    • Each cycle (counting pyruvate oxidation) produces 4 NADH, 1 FADH, 1 ATP
• Oxidative Phosophorylation
  • Oxygen likes to be reduced (electron acceptor) -> forms H2O at the end
  • NADH -> CoQ -> CytC -> … -> pumps H+ across the membrane -> O2 is the final electron acceptor -> forms H2O
  • Accounts for the majority of the ATPs produced (~28)
• Fermentation
  • Only uses glycolysis to generate ATP
  • Alcohol fermentation
  • Lactic acid fermentation (when O2 is scarce)
• How Other Molecules Enter The Catabolic Pathway
  • Proteins
    • Strip the NH3
    • Goes to kreb cycle
  • Fats
    • Fatty acids need an additional step called beta oxidation, which yield acetyl CoA

      Photosynthesis

• Photosynthesis Overview
  • Sunlight (photons) + CO2 + H2O -> carbohydrate + O2
  • Integral for life
  • Photosynthesis can be broken down into two stages
    • Light reaction (light dependent)
      • H2O -> O2
      • ATP, NADPH
    • Calvin cycle (light independent)
      • Needs CO2
      • Creates G3P
• Light Reaction
  • light + H2O -> ATP + NADPH + O2 (by-product)
  • Leaf -> mesophyll (interior tissue of the leaf) -> chloroplasts -> thykloid (little disks)
  • Lighr reaction takes place in thykloid membranes
    • Light goes to PS2 and PS1 (called the linear electron flow)
      • Photosystems consist of a reaction-center complex and a light-harvesting complex
    • Chlorophyll called P680 donates an electron, which then is used to pump protons
    • P680+ is an ion, which then grabs the electron from H2O. H2O gets broken down into 1/2 O2 (where the oxygen by-product comes from) and 2H+
    • Photophosorlation: Stroma has low H+ concentration gradient. Protons are pumped inside to the thykloid space.
    • PS1 has P700
      • The electron is used to reduce NADP+ to NADPH
      • P700 then gets the electron from the low-energy electron from P680
• Calvin Cycle
  • Uses the energy from ATP and NADPH to reduce CO2 to sugar
  • Anabolic
  • The carbohydrate produced directly from Calvin cycle is G3P, not glucose (cycle takes place 3 times)
  • Carbon fixation
    • Each CO2 molecule, one at a time, gets attached to a five-carbon sugar named RuBP
    • Rubisco is the enzyme that catalyzes the reaction
    • The result is a six-carbon sugar that gets split in half immediately -> 3-phosphoglycerate
  • Reduction
    • Each 3-phosphoglycerate receives an additional phosphate group from ATP
    • Eventually it becomes G3P
    • Note that for every 3 CO2, 6 G3P are formed, but only 1 can count as a net gain
  • Regeneration of the CO2 acceptor (RuBP)
    • The five molecules of G3P (worth 15 carbons) gets rearranged to 3 RuBPs
  • Consumes a total of 9 ATP and 6 NADPH
• Evolution of Alternative Mechanisms
  • Need to adapt to hot and arid climates
  • Photorespiration: Rubisco sometimes also fixes oxygen
    • Produces a two-carbon compound
  • C4 plants