CHAPTER 6-10 STUDY GUIDE  

What is plasma membrane?

∙ Make sure to review all figures from the power points  

∙ Words that are bolded are important and more likely to be tested

CHAPTER SIX: A TOUR OF THE CELL

Introduction to chapter six: The Fundamental Units of Life

∙ All organisms are made of cells (simplest collection of live matter)

∙ All cells descend from previous cells

Concept 6.1: Biologists use microscopes and the tools of biochemistry to study cells

∙ Microscopy  

o Light microscope (LM)- visible light passes through specimen then through glass lense  Lenses bend light which magnifies the image

o Parameters of microscopy:

 Magnification- real size v. image size

What is nuclear envelope?

We also discuss several other topics like Which situations are usually dealt with using positive reinforcement?

 Resolution- clarity

 Contrast- difference in brightness

∙ Review figure 6.2  

∙ Organelles- membrane-enclosed structures in eukaryotic cells  

∙ Know figure 6.3!  

o Brightfield  

o Phase-contrast

o Differential-interference-contrast

o Fluorescence

o Confocal

o Deconvolution

o Super-resolution

o Scanning electron microscopy  

 Focuses a beam of electrons onto specimen’s surface (3D image)

o Transmission electron microscopy  Don't forget about the age old question of What is the practice of using data from a sample and the rules of probability to make careful statements about the population from which the sample was drawn?

 Focus beam of electrons through a specimen to study internal structures of cells

∙ Cell Fractionation- takes cells apart and separates the major organelles from one another  Centrifuge  

What is lysosome?

We also discuss several other topics like Who are in charge of explaining price variances?

Concept 6.2: Eukaryotic cells have internal membranes that compartmentalize their functions.

∙ ALL cells have:

o Plasma membrane

o Cytosol (semifluid substance)

o Chromosomes (carry genes)

o Ribosomes (make proteins)

∙ Prokaryotic

o No Nucleus

o DNA in a nucleoid (unbound region)

o No membrane-bound organelles

o Cytoplasm bound by the plasma membrane

o Ex: Bacteria and Archaea

∙ Eukaryotic

o DNA in a nucleus that is bound by a nuclear envelope  

o Membrane-bound organelles  If you want to learn more check out How was liszt's "la campanella etude" utilized for communicating to the audience?

o Cytoplasm in the region between the plasma membrane and nucleus  If you want to learn more check out How do these factors influence attraction?

o Also (typically) much larger than prokaryotic cells

o Ex: Protista, Fungi, Animals, Plants

∙ Plasma membrane: selectively permeable barrier that allows oxygen, nutrients, and waste to go in and  out of the cell (hydrophobic region sandwiched between two hydrophilic regions)

∙ Metabolic requirements set upper limits on cell size (surface area to volume ratio- size increases, volume  grows proportionally more than it)

∙ Know the basic structures of the organelles.

Concept 6.3: The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by  the ribosomes

∙ Nucleus contains majority of cell’s genetic makeup (easiest to see as well)

 DNA is organized into units called chromosomes  

 Chromosomes are made of a single DNA molecule associated w/ proteins

 Chromatin= DNA + proteins (condenses to chromosomes as a cell divides)

 Nucleolus: site of ribosomal RNA synthesis (rRNA)- in nucleus  If you want to learn more check out What is ethnomedicine?

∙ Nuclear envelope: encloses nucleus and separates it from cytoplasm  

 Nuclear membrane each has lipid bilayer (double membrane)

 Pores regulate molecule entry & exit

 Envelop is lined by nuclear lamina- maintains the shape of the nucleus; made of  

proteins

∙ Ribosomes use DNA info to make proteins- protein synthesis- in two locations:

 Cytosol (free ribosomes)

 On outside of the endoplasmic reticulum or the nuclear envelope (bound ribosomes)

Concept 6.4: The endomembrane system regulates protein traffic and performs metabolic functions in  the cell

∙ Endomembrane system includes:

 Nuclear envelope

 Endoplasmic reticulum

 Golgi apparatus

 Lysosomes

 Vacuoles

 Plasma membrane

∙ All continuous/connected via transfer by vesicles

∙ Endoplasmic reticulum (ER): more than half the total membrane (in eukaryotic)- continuous w/ nuclear  envelope  

 Smooth ER:  

 lacks ribosomes

 synthesize lipids  

 Metabolize carbohydrates

 Store calcium ions

 Detoxifies drugs and poisons

 Rough ER:  

 Surface covered in bound ribosomes which secrete glycoproteins- proteins covalently  bonded to carbs.

 Distributes transport vesicles- secretory proteins surrounded by membranes  

 Membrane factory of the cell

∙ Golgi apparatus:  

 Made of cisternae- flattened membranous sacs

 Modifies products of the ER

 Manufactures specific macromolecules  

 Sorts & packages materials into transport vesicles  

 Cis face- “Receiving” side  

 Trans face- “shipping” side

∙ Lysosome: membranous sac of hydrolytic enzymes that can digest macromolecules  Its enzymes work best in acidic environment

 Rough ER makes  hydrolytic enzymes + lysosomal membranes  transferred to Golgi  Phagocytosis: cell engulfs another cell- “food vacuole”  then fuses w/ lysosome = digestion   They also use enzymes to recycle the cell’s own damaged organelles & macromolecules autophagy

∙ Vacuoles:  

 Derived from the ER & Golgi apparatus  

 Food vacuoles: formed by phagocytosis

 Contractile vacuoles: pump excess water out of cells  

 Found in freshwater protists

 Central vacuoles: holds organic compounds & water  

 Found in mature plant cells  

Concept 6.5: Mitochondria and chloroplasts change energy from one form to another

∙ Mitochondria & Chloroplasts:

 Similarities to bacteria-  

 Enveloped by double membrane

 Free ribosomes & circular DNA molecules

 Grow/reproduce almost independently of cell

2

 ^The above leads to the endosymbiont theory:  

 eukaryote ancestor engulfed an oxygen-using, non-photosynthetic prokaryotic cell  Engulfed cell formed endosymbiotic relationship w/ host cell

 The endosymbionts evolved into mitochondria  

 One of the cells may have taken up a photosynthetic prokaryoteevolved to chloroplasts ∙ Mitochondria:

 Site of cellular respiration  

 Smooth outer membrane & inner membrane folded into cristae (which creates a large surface  area for enzymes that synthesize ATP)

o Inner membrane has 2 compartments

 Intermembrane space

 Mitochondrial matrix- some metabolic steps of cellular respiration are  

catalyzed here

∙ Chloroplasts:

 Contain green pigment chlorophyll  

 Also has enzymes that function in photosynthesis

 Found in leaves, algae, & other green organs of plants

 Structure:

 Thylakoids: membranous sacs, stacked to form a granum/grana

 Stroma: the internal fluid

 Chloroplasts are in the group of plant organelles called plastids

Concept 6.6: The cytoskeleton is a network of fibers that organizes structures and activities in the cell

∙ Cytoskeleton: network of fibers extended throughout the cytoplasm

 Supports cell & maintains its shape  

 Anchors many organelles

 3 types of structures:

 Microtubules: thickest; hollow rods about 25 nm in diameter and about 200 nm to 25  microns long

 Shapes cell

 Guides movement of organelles

 Separates chromosomes during cell division

 Control the beating of flagella & cilia:  

 Microtubules sheathed by the plasma membrane

 Basal body anchors them

 Dynein, a motor protein, drives their bending movements

 Microfilaments (actin filaments): thinnest; two intertwined strands of actin 7 nm in  diameter  

 Cell shape (bear tension & resist pulling force)

 They form a 3D network called the cortex inside plasma membrane

 Muscle contraction  

 Cytoplasmic streaming: circular flow of cytoplasm within cells

 Speeds up distribution of materials

 In plant cells, actin-myosin/sol-gel transformations drive this

 Cell motility

 Contain the proteins myosin and actin

 Which drives amoeboid movement

 Cells crawl along surfaces by extending pseudopodia

 Make up the core of microvilli of intestinal cells

 Intermediate filaments: 8–12 nanometers; middle range

 Support cell shape

 Fix organelles in place  

 More permanent cytoskeleton fixtures

 Interacts w/ motor proteins to produce motility

 Vesicles can travel internally along its tracks

∙ Centrosomes: where microtubules grow near the nucleus, and each has a pair of… ∙ Centrioles: have nine triplets of microtubules arranged in a ring

Concept 6.7: Extracellular components and connections between cells help coordinate cellular  activities

∙ Cell wall: extracellular structure that distinguishes plant cells from animal cells

 Prokaryotes, fungi, and some unicellular eukaryotes also have cell walls

 Functions:

3

 Protects plant cell

 Maintains its shape

 Prevents taking up too much water

 Made of cellulose fibers inside other polysaccharides and proteins

 The layers of the cell wall

 Primary cell wall: thin & flexible

 Middle lamella: thin layer between primary walls  

 Secondary cell wall: (some cells) between plasma membrane & primary cell wall  Plasmodesmata: channels between adjacent plant cells  

∙ Extracellular matrix (ECM): covering of animal cells  

 Made of glycoproteins:  

 Collagen

 Proteoglycans

 Fibronectin

 These proteins bind to integrins, receptor proteins  

 Regulates cell behavior by communicating through integrins

 Influence gene activity in nucleus  

 Mechanical signaling may occur through cytoskeletal changes trigger chemical signals in the cell

∙ Cell Junctions: communication between direct physical contact among cells  

 3 types:

 Tight junctions: membranes of neighboring cells are pressed together, preventing  leakage of extracellular fluid

 Desmosomes: (anchoring junctions) fasten cells together into strong sheets

 Gap junctions: (communicating junctions) provide cytoplasmic channels between  adjacent cells

∙ Plasmodesmata: channels that perforate plant cell walls

 Allows water & small solutes (sometimes proteins and RNA) to pass between cells

4

CHAPTER SEVEN: MEMBRANE STRUCTURE AND FUNCTION  

Introduction to chapter seven: Life at the Edge

∙ Plasma membrane separates cells from surroundings  

∙ Exhibits selective permeability: allowing some substances to cross it more easily than others Concept 7.1: Cellular membranes are fluid mosaics of lipids and proteins

∙ Phospholipids

 Most abundant lipid in plasma membrane  

 Amphipathic: hydrophobic and hydrophilic regions

 Phospholipid bilayer exists as a stable boundary between two aqueous compartments  Can move within bilayer  

 Most of the lipids, and some proteins, drift laterally (& rarely transversely)

∙ Fluid mosaic model: a membrane is a fluid structure with a “mosaic” of proteins within it  Proteins are not randomly distributed in membrane

∙ Fluidity of Membrane

 Cool temperatures= membranes go from fluid state solid state

 The solidifying temp. depends on types of lipids

 Membranes rich in unsaturated fatty acids= more fluid than those rich in saturated fatty  acids

 Membranes must be (oil-like) fluid to work properly

 The steroid, cholesterol: different effects on membrane fluidity @ diff. temperatures  Warm temps. (such as 37°C): cholesterol restrains movement of phospholipids

 Cool temps.: maintains fluidity by preventing tight packing

∙ Membrane Proteins

 Membrane= collage of different proteins embedded in the fluid matrix of the lipid bilayer  Proteins determine function

 Peripheral proteins: bound to surface of membrane  

 Integral proteins: infiltrates the hydrophobic core  

 Ones that span the membrane= transmembrane proteins

 Its hydrophobic regions consist of stretches of nonpolar

amino acids, often coiled into alpha helices

 6 membrane protein functions:

 Transport

 Enzymatic activity

 Signal transduction

 Cell-cell recognition

 Intercellular joining

 Attachment to the cytoskeleton and extracellular matrix (ECM)

 HIV must bind to the immune cell surface protein CD4 and a “co-receptor” CCR5 in order to infect a cell  

 HIV cannot enter the cells of resistant individuals that lack CCR5

∙ Membrane Carbohydrates  

 Cells recognize other cells by binding to molecules, typically w/ carbohydrates, on the outside  surface of the plasma membrane

 Membrane carbohydrates may be covalently bonded to lipids = (glycolipids) or more commonly  to proteins= (glycoproteins)

Concept 7.2: Membrane structure results in selective permeability

∙ Lipid bilayer permeability  

 Hydrophobic (nonpolar) molecules, such as hydrocarbons, can dissolve in the lipid bilayer and  pass through the membrane rapidly

 Hydrophilic molecules including ions and polar molecules do not cross the membrane easily ∙ Transport proteins: allow passage of hydrophilic substances across the membrane  Channel proteins: have a hydrophilic channel used as a tunnel for molecules  

 Aquaporins: channel proteins that facilitate the passage of water

 Carrier proteins: bind to molecules & change shape to shuttle them across the membrane 5

 A transport protein is specific for the substance it moves

Concept 7.3: Passive transport is diffusion of a substance across a membrane with no energy  investment

∙ Diffusion: the tendency for molecules to spread out evenly into the available space  Molecules move randomly but diffusion happens directionally  

 Dynamic equilibrium: as many molecules cross the membrane in one direction as in the other  Concentration gradient: region where density of a chemical substance increases or decreases  Substances diffuse down their concentration gradient  

 Passive transport: no energy is expended by the cell to make diffusion happen

 Ex.- The diffusion of a substance across a biological membrane

∙ Osmosis: diffusion of water across a selectively permeable membrane

 Water diffuses from regions of low solute to high solute until solute concentration is equal on both  sides

 Tonicity: ability of a surrounding solution to cause a cell to gain or lose water

 Isotonic solution: Solute concentration is the same as that inside the cell; no net water  movement across the plasma membrane

 Hypertonic solution: Solute concentration is greater on outside than inside; cell loses water  Hypotonic solution: Solute concentration is less on outside than inside; cell gains water  Osmoregulation: the control of solute concentrations and water balance

∙ Water balance  

 Cell walls help maintain water balance

 Turgid (hard): A plant cell in a hypotonic solution swells until the wall opposes uptake  Flaccid (limp): If a plant cell and its surroundings are isotonic, there is no net movement of  water into the cell

 Plants lose water in hypertonic solutions  

 Plasmolysis: membrane pulls away from the cell wall causing the plant to wilt (lethal) ∙ Facilitated diffusion: transport proteins (channel & carrier) speed the passive movement of molecules  across the plasma membrane

 Still passive because the solute moves down its concentration gradient, and the transport  requires no energy

 Ion channels: facilitate the diffusion of ions  

 Gated channels: open or close in response to a stimulus

Concept 7.4: Active transport uses energy to move solutes against their gradients

∙ Active transport: moves substances against their concentration gradients

 Requires energy (ATP)

 Performed by specific proteins in the membranes

 Allows cells to maintain concentration gradients that differ from their surroundings

 Sodium-potassium pump: one type of active transport system

1. Cytoplasmic Na+ binds to the sodium- potassium pump. The affinity for Na+ is high when the  protein has this shape.

2. Na+ binding stimulates phosphorylation by ATP.

3. Phosphorylation leads to a change in protein shape, reducing its affinity for Na+, which is  released outside.

4. The new shape has a high affinity for K+, which binds on the extracellular siderelease of the  phosphate group

5. Loss of the phosphate group restores the protein’s original shape, which has a lower affinity  for K+.

6. K+ is released; affinity for Na+ is high again, and the cycle repeats.

∙ Membrane potential: voltage difference across a membrane

 Voltage is created by differences in the distribution of positive and negative ions across a  membrane

 Two combined forces, collectively called the electrochemical gradient, drive the diffusion of  ions across a membrane

 Chemical force: from ion’s concentration gradient

 Electrical force: form the effect of the membrane potential on the ion’s movement

 Electrogenic pump: transport protein that generates voltage across a membrane  The sodium-potassium pump = major electrogenic pump of animal cells

 Proton pump = main electrogenic pump of plants, fungi, and bacteria  

 helps store energy that can be used for cellular work

∙ Cotransport: occurs when active transport of a solute indirectly drives transport of other substances  6

 Plants commonly use the gradient of hydrogen ions generated by proton pumps to drive active  transport of nutrients into the cell

Concept 7.5: Bulk transport across the plasma membrane occurs by exocytosis and endocytosis

∙ Bulk transport requires energy

 Large molecules- cross membrane in bulk via vesicles

 Small molecules and water- enter/leave the cell through lipid bilayer or via transport proteins ∙ Exocytosis: transport vesicles migrate to membranefuse with itrelease contents outside the cell  Secretory cells use exocytosis to export their products

∙ Endocytosis: cell takes in macromolecules by forming vesicles from the plasma membrane  Reversal of exocytosis, involving different proteins

 There are three types of endocytosis

 Phagocytosis (“cellular eating”)

 Cell engulfs a particle in a vacuole

 Vacuole fuses w/ lysosome to digest the particle

 Pinocytosis (“cellular drinking”)

 Molecules dissolved in droplets are taken up when extracellular fluid is “gulped”

into tiny vesicles

 Receptor-mediated endocytosis

 Binding of ligands to receptors triggers vesicle formation

 Ligand: any molecule that binds specifically to a receptor site of another  

molecule

7

CHAPTER EIGHT: AN INTRODUCTION TO METABOLISM  

Introduction to chapter eight: The Energy of Life  

∙ The cell extracts energy stored in sugars and other fuels & applies energy to perform work ∙ Some organisms even convert energy to light (bioluminescence)

Concept 8.1: An organism’s metabolism transforms matter and energy, subject to the laws of  thermodynamics

∙ Metabolism: the totality of an organism’s chemical reactions

 Metabolic pathway: begins w/ specific molecule & ends w/ a product

 Each step is catalyzed by a specific enzyme

 Catabolic pathways: release energy by breaking down complex molecules into simpler  compounds

 Ex: Cellular respiration- the breakdown of glucose in the presence of oxygen

 Anabolic pathways: consume energy to build complex molecules from simpler ones  Ex: The synthesis of protein from amino acids  

 Bioenergetics: the study of how energy flows through living organisms

∙ Energy: the capacity to cause change

 Kinetic energy: energy of motion

 Heat (thermal energy): kinetic energy of random movement of atoms/molecules  Potential energy: energy that matter possesses b/c of its location or structure

 Chemical energy: potential energy available for release in a chemical reaction

 Energy can be converted from one form to another

∙ Laws of Energy Transformation  

 Thermodynamics: study of energy transformations

 An isolated system cannot exchange energy/matter w/ its surroundings

 Open system: energy and matter transferred between the system & its surroundings  Organisms are open systems

 First law of thermodynamics (principle of conservation of energy): the energy of the universe  is constant

 Energy can be transferred and transformed, but it cannot be created or destroyed

 Some energy is unusable in transfer/transformation, and is lost as heat

 Second law of thermodynamics:

 Every energy transfer or transformation increases the entropy (disorder) of the universe  Cells convert organized energy to heat

 Spontaneous processes: occur w/o energy input

 To occur w/o energy input- must increase entropy of universe

∙ Order vs. Disorder

 Cells create ordered from less ordered stuff

 Organisms replace ordered forms w/ less ordered forms of energy & matter

  Energy flows into an ecosystem in the form of light and exits in the form of heat 

 Entropy (disorder)- decrease in organism, but universe’s total entropy increases

Concept 8.2: The free-energy change of a reaction tells us whether or not the reaction occurs  spontaneously

∙ Free-energy: energy that can do work when temperature and pressure are uniform  ∆G (the change in free energy) = ∆H (change in total energy) – T (temperature in Kelvin)∆S  (change in entropy)

  Only processes with a negative ∆ G are spontaneous 

 Spontaneous processes:

 Free energy decreases  

 Stability of a system increases

 The released free energy can be harnessed to do work

 Measure of a system’s instability

 Equilibrium = state of maximum stability

∙ Exergonic reaction: release of free energy (spontaneous)

8

∙ Endergonic reaction absorbs free energy (nonspontaneous)

∙ Reactions in closed systemreach equilibriumdo no work

 Cells: not equilibrium; open systems  

 Metabolism is never at equilibrium

 Catabolic pathway: (cell)- releases free energy in a series of reactions

Concept 8.3: ATP powers cellular work by coupling exergonic reactions to endergonic reactions

∙ Work in cells

 3 kinds

 Chemical  

 Transport

 Mechanical  

 Energy coupling: using an exergonic process to drive an endergonic one

 Cells manage energy resources this way

 Mediated by ATP

∙ ATP (adenosine triphosphate): cell’s energy shuttle

 Composed of ribose (a sugar), adenine (a nitrogenous base), and 3 phosphate groups  The bonds between the phosphates broken by hydrolysis

 Energy is released when these bonds break from:

 change to a state of lower free energy, not from the bonds themselves

 Cellular work is powered by ATP  

 Energy form exergonic (hydrolysis) powers endergonic  

 Coupled reactions are exergonic overall  

 ATP drives endergonic reactions by:

 Phosphorylation: transferring a phosphate group to another molecule

 Phosphorylated intermediate: recipient molecule  

 ATP hydrolysischange in protein shape & binding ability

∙ Regeneration of ATP

 ATP = renewable resource regenerated by adding phosphate to adenosine diphosphate (ADP)  Catabolic reactions in the cellEnergy to phosphorylate ADP  

Concept 8.4: Enzymes speed up metabolic reactions by lowering energy barriers

∙ Catalyst: Chemical agent speeds up a reaction w/o being consumed

 Ex: Hydrolysis of sucrose by the enzyme sucrase  

∙ Enzyme: catalytic protein

 Catalyze reactions by lowering the EA barrier by:

 Orienting substrates correctly

 Straining substrate bonds

 Providing a favorable microenvironment

 Covalently bonding to the substrate

 Do not affect ∆G

 Substrate: the reactant that an enzyme acts on

 Enzyme-substrate complex: when the enzyme binds to its substrate  

 Enzyme activity if affected by:

 Environmental factors- temp & pH

 Each enzyme has an optimal temp. to function

 And optimal pH  

 Chemicals that influence the enzyme  

∙ Activation energy (free energy of activation): initial energy needed to start a chemical reaction   Often supplied as thermal energy  

 Active site: region on enzyme where substrate binds

 Induced fit: brings chemical groups of active site into places that increase ability to catalyze the  reaction

 Enzymatic reaction: substrate binds to active site of enzyme

1. Substrates enter active site.

2. Substrates are held in active site by weak interactions.

3. Substrates are converted to products.

4. Products are released.

5. Active site is available for new substrates.

∙ Cofactors: non-protein enzyme helpers

9

 May be inorganic (metal in ionic form) or organic

 Coenzyme: organic cofactor  

 Include vitamins

∙ Enzyme inhibitors  

 Competitive inhibitors: bind to the active site of an enzyme (competes w/ substrate)  Noncompetitive inhibitors: bind to another part of an enzymeenzyme changes shape &  makes active site less effective

 Ex: toxins, poisons, pesticides, and antibiotics

∙ Evolution of enzymes

 Enzymes: proteins encoded by genes

 Mutations= Changes in amino acid composition of an enzyme

 May result in different enzyme activity…

 Or altered substrate specificity

 New environmental conditions = new favored form of enzyme

 Ex: 6 amino acid changes improved substrate binding and breakdown in E. coli

Concept 8.5: Regulation of enzyme activity helps control metabolism

∙ Allosteric regulation: inhibits or stimulates an enzyme’s activity

 Occurs when regulatory molecule binds to protein at one site & affects the protein’s function at  another site

 Most allosterically regulated enzymes are made from polypeptide subunits

 Each enzyme has active and inactive forms

 The binding of an activator stabilizes the active form of the enzyme

 The binding of an inhibitor stabilizes the inactive form of the enzyme

 Cooperativity: amplifies enzyme activity  

 One substrate molecule primes an enzyme to act on other substrate molecules more  readily

 It’s allosteric b/c binding by a substrate to one active site affects catalysis in a different  active site

∙ Feedback inhibition: end product of metabolic pathway shuts down the pathway  Prevents cell from wasting chem. resources by  

 synthesizing more product than needed

 Structures within cell help bring order to metabolic pathways

 Some enzymes act as structural components of membranes

 Eukaryotic cells: some enzymes reside in specific organelles

 Ex: enzymes for cellular respiration are located in mitochondria

10

CHAPTER NINE: CELLULAR RESPIRATION AND FERMENTATION

Introduction to chapter nine: Life is Work

∙ Energy flows into an ecosystem as light and exits as heat

∙ Photosynthesis generates O2 & organic molecules (used in cellular respiration)

∙ Cells use chem. energy to generate ATP

Concept 9.1: Catabolic pathways yield energy by oxidizing organic fuels

∙ Catabolic pathways: release stored energy by breaking down complex molecules  

 Electron transfer plays a major role in these pathways

 These processes are central to cellular respiration

 The breakdown of organic molecules is exergonic

 Fermentation: partial degradation of sugars that occurs w/o O2

 Aerobic respiration: consumes organic molecules and O2 & yields ATP

 Similar to aerobic respiration but consumes compounds other than O2

 Cellular respiration: both aerobic and anaerobic respiration but often referred to as just aerobic  respiration

 It helps to trace cellular respiration with glucose

 C6H12O6 + 6 O2 → 6 CO2 + 6 H2O + Energy (ATP + heat)

∙ Redox Reactions: (oxidation-reduction reactions)- chemical reactions that transfer electrons between  reactants  

 The release of energy during the transfer of electrons synthesizes ATP

 In cellular respiration: glucose is oxidized & O2 is reduced

 Oxidation: loses electrons (oxidized)

 Reduction: gains electrons (reduced)  

 LEO GER (LoseElectronsOxidation GainElectronsReduction)

 Reducing agent: electron donor

 Oxidizing agent: electron receptor  

 Some redox reactions do not transfer electrons but change the electron sharing in covalent bonds  Ex: reaction between methane & O2

∙ NAD+ and Electron Transport Chain

 Electrons from organic compoundsfirst transferred to NAD+: a coenzyme

 NAD+ functions as an oxidizing agent during cellular respiration

 Each NADH (the reduced form of NAD+) represents stored energy that is used to synthesize ATP  NADH  passes electrons to the electron transport chain

 Which passes electrons in a series of steps  

 O2 pulls electrons down the chain in an energy-yielding tumble

 The energy yielded is used to regenerate ATP

∙ Stages of Cellular Respiration

 Glycolysis: breaks down glucose into two molecules of pyruvate

 Citric acid cycle (Krebs Cycle): completes the breakdown of glucose

 Oxidative phosphorylation: accounts for most of the ATP synthesis

 Accounts for 90% of ATP generated by cellular respiration  

 For each glucose, the cell makes up to 32 molecules of ATP  

Concept 9.2: Glycolysis harvests chemical energy by oxidizing glucose to pyruvate

∙ Glycolysis: sugar splitting (very ancient cellular process)

 Breaks down glucose into 2 pyruvates

 Occurs in the cytoplasm & has two major phases:

 Energy investment phase

Know figure 9.9a:

1. Glucose

(ATP goes in, ADP out)

2. Glucose 6-phosphate

3. Fructose 6-phosphate

(ATP goes in, ADP out)

4. Fructose 1,6-biphosphate

5. Glyceraldehyde 3-phosphate (G3P) OR Dihydroxyacetone phosphate (DHAP)

 Energy payoff phase

Know figure 9.9b:

6. Glyceraldehyde 3-phosphate (G3P)

11

(2 NAD+ goes in, and 2 NADH and 2H+ comes out)

7. 1,3-Bisphosphoglycerate

(2 ADP goes in, and 2 ATP goes out)

8. 3-Phosphoglycerate

9. 2-Phosphoglycerate

(2 H2O out)

10. Phosphoenolpyruvate (PEP)

(2 ADP in, and 2 ATP out)

11. Pyruvate

 Glycolysis occurs with or without O2

Concept 9.3: After pyruvate is oxidized, the citric acid cycle completes the energy-yielding oxidation of organic molecules

∙ Pyruvate enters the mitochondrion in the presence of O2 oxidation of glucose is completed ∙ Acetyl CoA: pyruvate is converted to this coenzyme that links glycolysis to the citric acid cycle  Carried out by a multi-enzyme complex that catalyzes three reactions

∙ Citric Acid Cycle (Krebs cycle): completes the breakdown of pyruvate to CO2

 Oxidizes organic fuel derived from pyruvate 1 ATP, 3 NADH, and 1 FADH2 per turn

 8 steps of the citric acid cycle: (draw figure 9.12!)

1. acetyl CoA joins the cyclecombines w/ oxaloacetate

2. CitrateH2O goes out then back in

3. Isocitrate NAD+ goes in & NADH+H+ & CO2 come out

4. α-KetoglutarateCoA-SH & NAD+ go in, and CO2 & NADH+H+ come out

5. Succinyl CoA CoA & GTP out and phosphate & GDP in creates ATP

6. Succinate FDH in & FADH2 out

7. Fumarate H2O in

8. MalateNAD+ in & NADH + H+ out back to step one

Concept 9.4: During oxidative phosphorylation, chemiosmosis couples electron transport to ATP  synthesis

∙ Electron Transport Path

 NADH and FADH2 from the citric acid cycle transfer electrons to

 Electron transport chain

 Electrons pass through many proteins

 Including cytochromes (each w/ iron) to O2

 Transfers no ATP directly  

 BUT releases energy in small amounts in each step of free energy drop  

 (from food to O2)

∙ Chemiosmosis: the use of energy in a H+ gradient to drive cellular work  

 Electron transferproteins pumping out H+ from matrix to intermembrane

 ATP Synthase: uses flow of H+ moving back across membrane through protein complex to drive  phosphorylation of ATP  

 This movement couples the redox reactions of electron transport chainATP synthesis  H+ gradient= proton-motive force: emphasizes capacity to do work

 Be familiar with figure 9.14 and 9.15

∙ Overview of ATP through Cellular Respiration:

 Glucose  NADH  electron transport chain  proton-motive force ATP 

 Makes about 32 ATP  

Concept 9.5: Fermentation and anaerobic respiration enable cells to produce ATP without the use of  oxygen

∙ Fermentation: uses a final electron acceptor (NOT O2) in electron transport chain

 Consists of glycolysis + reactions = NAD+reused by glycolysis

 2 types:

 Alcohol fermentation: pyruvate converted to ethanol:

1. Release CO2

2. Produce ethanol

 Alcohol fermentation by yeast= brewing, winemaking, and baking

 Lactic acid fermentation: pyruvate is reduced by NADH lactate as end product

 Does not release CO2  

 Fungi and bacteria lactic acid fermentation cheese and yogurt

12

 Human muscle cellsO2 is scarcelactic acid fermentationATP

 Produces 2 ATP per glucose

∙ Anaerobic respiration: uses substrate-level phosphorylation to generate ATP (NO electron transport  chain at all)

 Obligate anaerobes: carry out fermentation or anaerobic respiration and cannot survive in the  presence of O2

 Yeast & many bacteria = facultative anaerobes: survive using fermentation or cellular  respiration

 Pyruvate- leads to 2 alternative catabolic routes

Concept 9.6: Glycolysis and the citric acid cycle connect to many other metabolic pathways

∙ Catabolism

 Catabolic pathways- funnel electrons from organic molecules cellular respiration

 Glycolysis accepts wide range of carbs.

 Proteins- digested to amino acids; amino groups- feed glycolysis or citric acid cycle  Fats- digested to glycerol (used in glycolysis) & fatty acids- (used in generating acetyl CoA)   Fatty acids- broken down by beta oxidation & yield acetyl CoA

 Oxidized gram of fat = 2x as much ATP as oxidized gram of carbohydrate

 Be familiar with Figure 9.19

∙ Feedback in Cellular Respiration

 Feedback inhibition= metabolic control

 ATP lowrespiration speeds up OR ATP highrespiration slows down

 Control of catabolism- regulating activity of enzymes @ points in the catabolic pathway  Know figure 9.20

13

CHAPTER TEN: PHOTOSYNTHESIS

Intro to chapter ten: The Process That Feeds the Biosphere

∙ Photosynthesis: converts solar energy  chemical energy

 Occurs in plants, algae, certain other unicellular eukaryotes, & some prokaryotes

∙ Autotrophs: self-sustaining (don’t eat other organisms)  

 Producers of biosphere- CO2 + inorganic molecules = organic molecules  

 Many plants are photoautotrophs: use sunlight (energy)  organic molecules

∙ Heterotrophs: obtain organic material from other organisms

 Consumers of biosphere

 Depend on photoautotrophs for food and O2

∙ Earth’s supply of fossil fuels was formed from the remains of organisms that died hundreds of millions of  years ago

Concept 10.1: Photosynthesis converts light energy to the chemical energy of food

∙ Chloroplasts: (evolved from photosynthetic bacteria), hence the site of photosynthesis  Has envelope of 2 membranes surrounding the stroma: dense fluid  

 Split H2O into hydrogen & oxygen; hydrogen electrons  sugar molecules & release O2 as by product

 Leaves are the major locations of photosynthesis

 Found mesophyll cells: the interior tissue of the leaf

 Each mesophyll cell contains 30–40 chloroplasts

 CO2 enters & O2 exits the leaf through the stomata

 Thylakoids: are connected sacs in the chloroplast which compose a third membrane system  May be stacked in columns called grana

 Chlorophyll: pigment that makes leaves green- in thylakoid membranes

∙ Photosynthesis

 Photosynthesis equation:

6 CO2 + 12 H2O + Light energy → C6H12O6 + 6 O2 + 6 H2O  

 Reverse of cellular respiration

 Know figure 10.5: Photosynthesis Redox

 Photosynthesis- reverses direction of electron flow compared to respiration

 Photosynthesis- redox process; H2O oxidized & CO2 reduced

 Photosynthesis- endergonic process

∙ Stages of Photosynthesis:

 Photosynthesis- light reactions (photo) & Calvin cycle (synthesis)

 The light reactions (in the thylakoids)

 Split H2O

 Release O2

 Reduce the electron acceptor NADP+ to NADPH

 Generate ATP from ADP by photophosphorylation

 The Calvin cycle (in the stroma)- uses ATP & NADPH from CO2 sugar  

 Begins with carbon fixation: using CO2 in organic molecules

 Know Figure 10.6

Concept 10.2: The light reactions convert solar energy to the chemical energy of ATP and NADPH

∙ Sunlight

 Light: electromagnetic energy/radiation

 Behaves like it has discrete particles- photons

 Light travels in rhythmic waves

 Wavelength: distance between crests of waves

 Determines type of electromagnetic energy

 Electromagnetic spectrum: entire range of electromagnetic energy/radiation  

 Visible light: consists of wavelengths that produce colors we can see

 Includes photosynthesis

∙ Photosynthetic pigments

 Pigments: substances that absorb visible light

 Different pigments absorb different wavelengths

14

 Wavelengths that are not absorbed are reflected or transmitted

 Leaves appear green b/c chlorophyll reflects & transmits green light

 Spectrophotometer: measures a pigment’s ability to absorb wavelengths  

 Sends light through pigments & measures fraction of light transmitted @ each  

wavelength

 Absorption spectrum: graph plotting pigment’s light absorption vs. wavelength

 The absorption spectrum of chlorophyll a: violet-blue and red light work best for  

photosynthesis

 Chlorophyll a = main photosynthetic pigment

 Chlorophyll b: Accessory pigment that broadens spectrum used for photosynthesis  The difference in the absorption spectrum between chlorophyll a and b is from  

slight structural differences between the pigment molecules  

 Carotenoids: accessory pigments function in photo-protection

 Absorb excessive light that would damage chlorophyll

 Action spectrum: profiles relative effectiveness of diff. wavelengths of radiation in a process  First demonstrated in 1883 by Theodor W. Engelmann

 In his experiment, he exposed diff. segments of a filamentous alga to wavelengths

 Areas receiving wavelengths favorable to photosynthesis produced excess O2

 Used growth of aerobic bacteria along the alga as a measure of O2 production

 Understand Figure 10.11

∙ Chlorophyll gets excited!

 Pigment absorbs light = ground state excited state (unstable)

 Excited electrons  ground state = photons given off= afterglow called fluorescence  If illuminated, an isolated solution of chlorophyll will fluoresce, giving off light & heat ∙ Photosystem: consists of a-

 Reaction-center complex: (a type of protein complex) surrounded by light-harvesting  complexes

 The light-harvesting complexes: (pigment molecules bound to proteins) transfer the  energy of photons to the reaction center

 Know figure 10.13

 A primary electron acceptor: Accepts excited electrons & reduced as a result

 Ex: Solar-powered transfer of an electron from a chlorophyll a molecule to the primary  electron acceptor is the first step of the light reactions

 There are two types of photosystems in the thylakoid membrane

1. Photosystem II (PS II) happens first (#’s reflect order of discovery) & best at absorbing a  wavelength of 680 nm

 The reaction-center chlorophyll a of PS II is called P680

2. Photosystem I (PS I) is best at absorbing a wavelength of 700 nm

 The reaction-center chlorophyll a of PS I is called P700

∙ Linear electron flow: the primary pathway, involves both photosystems and produces ATP and NADPH  using light energy

 There are 8 steps in linear electron flow:

1. Photon hits pigment & energy is passed among pigment molecules until it excites P680 2. Excited electron from P680transferred to the primary electron acceptor (Now called P680+) 3. H2O is split by enzymes, & electrons transferred from hydrogen atoms to P680+; reduces it to  P680

 P680+- strongest known biological oxidizing agent

 O2- released as a by-product reaction

4. Each electron goes down electron transport chain from primary electron acceptor of PS IIPS I 5. Energy released by the fall= creation of proton gradient across thylakoid membrane  Diffusion of H+ (protons) across the membrane drives ATP synthesis

6. In PS I (like PS II), transferred light energy excites P700, which loses an electron to an  electron acceptor

 P700+ (P700 that is missing an electron) accepts an electron passed down from PS II  via the electron transport chain

7. Each electron goes down electron transport chain from the primary electron acceptor of PS I  to the protein ferredoxin (Fd)

8. Electrons transferred to NADP+ & reduce it to NADPH

 The electrons of NADPH are available for the reactions of the Calvin cycle

∙ Cyclic electron flow: electrons cycle back from Fd to the PS I reaction center

 Uses only photosystem I and produces ATP, NOT NADPH

 No oxygen released

 Thought to have evolved before linear electron flow

 Protect cells from light-induced damage

 Some organisms have PS I but not PS II

 Ex: purple sulfur bacteria

15

∙ Chemiosmosis- Mitochondria vs. Chloroplasts

 In summary, light reactions generate ATP and increase the potential energy of electrons by  moving them from H2O to NADPH

Chloroplast

Both

Mitochondria

transform light energy into the chemical energy of ATP

protons pumped into thylakoid space & drive ATP synthesis  then diffuse back into stroma

generate ATP by  

chemiosmosis

transfer chemical energy from  food to ATP

protons are pumped to  

intermembrane space & drive  ATP synthesis then diffuse  back into mitochondrial matrix

Concept 10.3: The Calvin cycle uses the chemical energy of ATP and NADPH to reduce CO2 to sugar

∙ The Calvin cycle, like the citric acid cycle, regenerates its starting material after molecules enter and leave the cycle

 Builds sugar from smaller molecules by using ATP & reducing power of electrons carried by  NADPH

 Carbon enters cycle as CO2 & leaves as sugar- glyceraldehyde 3-phospate (G3P)  Cycle take place 3x fixing 3 molecules of CO2 Net synthesis of 1 G3P

 The Calvin cycle has three phases

1. Carbon fixation (catalyzed by rubisco)

2. Reduction

3. Regeneration of the CO2 acceptor (RuBP)

 KNOW figure 10.19

Concept 10.4: Alternative mechanisms of carbon fixation have evolved in hot, arid climates

∙ Photorespiration: rubisco adds O2 instead of CO2 in the Calvin cycle, producing a two-carbon compound  On hot, dry days, plants close stomata Conserves H2O BUT limits photosynthesis

 Reduces access to CO2 & causes O2 build up

 These conditions favor an apparently wasteful process called photorespiration

 In most plants (C3 plants), initial fixation of CO2, via rubisco, forms a three-carbon compound (3-phosphoglycerate)

 Photorespiration consumes O2 & organic fuel & releases CO2 w/o producing ATP or sugar  May be an evolutionary relic because rubisco first evolved at a time when the  

atmosphere had far less O2 and more CO2

 Limits damaging products of light reactions that build up in the absence of the  

Calvin cycle  

 Problem b/c on a hot, dry day it can drain 50% of the carbon fixed by the Calvin  

cycle

∙ C4 plants: minimize the cost of photorespiration by incorporating CO2 into four-carbon compounds   2 types of cells in leaves of C4 plants:

 Bundle-sheath cells: arranged in tightly packed sheaths around the veins of the  leaf

 Mesophyll cells: loosely packed between the bundle sheath & the leaf surface

 Sugar production in C4 plants 3-step process:

1. The production of the four carbon precursors is catalyzed by the enzyme PEP carboxylase  in the mesophyll cells  

 PEP carboxylase likes CO2 more than rubisco does; it can fix CO2 even when CO2

concentrations are low

2. These four-carbon compounds are exported to bundle-sheath cells

3. Within the bundle-sheath cells, they release CO2 that is then used in the Calvin cycle  Since the Industrial Revolution in the 1800s, CO2 levels have risen greatly

16

 Increasing levels of CO2 may affect C3 and C4 plants differently, perhaps changing the relative  abundance of these species

 The effects of such changes are unpredictable and a cause for concern

∙ CAM plants: open their stomata at night, incorporating CO2 into organic acids

 Some plants use crassulacean acid metabolism (CAM) to fix carbon

 Ex: succulents  

 Stomata close during the day, and CO2 is released from organic acids and used in the Calvin cycle  BE FAMILIAR WITH FIGURES 10.23a-c

17