BIOLOGY

Types of variables:

• Quantitative vs Qualitative

  • Quantitative: A variable you can measure

  • Qualitative: A variable you can observe

• Independent vs Dependent

  • Independent: The variable we control

  • Dependent: The variable we measure/observe; we think it depends on the independent variable

  • Abbreviated IV and DV

Control group: Group where nothing is being changed

Experimental group: Group where you change the independent variable

Hypotheses:

• Not a guess

• Proposed explanation for something

• Based on what we know

What are some types of intermolecular forces?

• Dispersion forces/Van Der Waals forces

• Electromagnetic attractions

• Dispersion forces

• Dipole-dipole forces

Hydrogen bonds

• H-bonds in water form between partially positive hydrogen & partially negative oxygen

• NOT the term for a covalent bond involving hydrogen

• Gives water special properties

• Important for structure of macromolecules

Special water properties

• High heat capacity

• High heat of vaporization

• High heat of fusion

• Cohesion/adhesion

Most common elements in biological systems: C, H, O, N, P, S (Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus, Sulfur)

Organic Chemistry: subset of chemistry that deals with organic compounds

Organic: contains carbon & oxygen

Macromolecules

• Most compounds fall into 1 of 4 groups of macromolecules

• Macromolecule: very large molecule, often with complex properties

• Most (but not all) macromolecules = polymers

• Polymer: long series of repeated units (monomers)

Making and Breaking Polymers

• Forming + breaking down polymers involves removing or adding a water molecule

• Make polymers via dehydration synthesis or condensation reaction

• Break down polymers via hydrolysis

Classes of Macromolecules

• 4 main types

  • Carbohydrates

    • Basic unit: monosaccharide (aka simple sugar) Ex: glucose

    • Polymer form: polysaccharide (aka complex sugar/carb)

    • Contain C, H, O (usually in 1:2:1 ratio)

    • Carbohydrate Functions

      • Energy

        • Glucose main substrate of cellular respiration

        • Short-term storage

          • Glycogen in animals

          • Starch in plants

      • Structure

        • Cellulose in plants (cell walls)

        • Chitin in animals

      • Signaling/communication

  • Nucleic acids

    • Basic unit: nucleotide

      • Basic structure:

        • 5-carbon sugar

        • Phosphate group

        • Nitrogenous group (5 of them)

          • Thymine (DNA)

          • Adenine (DNA & RNA)

          • Cytosine (DNA & RNA)

          • Guanine (DNA & RNA)

          • Uracil (RNA)

    • Polymer: no special term

    • Contains: C, H, O, N, P

    • 2 main types

      • DNA

      • RNA

      • DNA vs RNA

• Both nucleic acids

• 3 main diffs.

  • DNA = double stranded, RNA = single-stranded

  • DNA has thymine, RNA has uracil

  • DNA's sugar = deoxyribose, RNA'S = ribose

• Both present in all living cells

  • Nucleic Acid Function

    • Information

• • Lipids

    • Contains C, H, O, sometimes P

    • Largely hydrophobic

    • Hydrophobic: "water-fearing" doesn't mix well w/ water (other term is hydrophilic "water-loving"

    • 3 main types, each w/ special function

      • Triglycerides

        • AKA fats and oils

        • Main function: long-term energy storage

        • Glycerol + 3 fatty acids

        • Saturated vs unsaturated

          • Saturated fats have no C-C double bonds; tend to be solid, animal fat

          • Unsaturated fats have C-C double bonds; tend to be liquid, plant fat

      • Phospholipids

        • Like triglycerides, but 1 fatty acid replaced w/ phosphate

        • Changes nature of lipid!

          • Fatty acids = hydrophobic, phosphates = hydrophilic

          • Phospholipids want to be both

        • Will naturally create bilayer (origin of cell membrane)

        • Function: make up cell membrane

      • Steroids

        • Distinctive structure: 4 fused carbon rings

        • Little functional group additions give properties

        • Primary function: signaling, regulation (think hormones)

        • Also plays role in cell membranes

  • Proteins

    • Contains C, H, O, N, S

    • Monomer: amino acids

      • 20 amino acids

      • 4 basic parts

        • Central carbon w/ hydrogen

        • Carboxyl group

        • Amino group

        • R-group

          • The 20 amino acids vary in their R-group or sidechain

          • R-group = functional group

          • Gives amino acid its properties

          • Properties determine shape/function of whole protein

          • R-group interactions

            • Hydrophobic/hydrophilic interactions

            • Ionic attractions

            • H-bonding

            • Disulfide bridges

            • All of these give a protein its shape, and the shape of a protein determines its function

            • Denature: alter interactions/shape of protein... loss/change in function

    • Polymer: polypeptide

    • Layers of Structure

      • Analogy: Layers of structure of a book

        • 1. String of letters (thecatjumpsoverthelazydog)

        • 2. Recognizable subunits: words (cat the jumps over lazy the dog)

        • 3. Repeated structures: sentence (the cat jumps over the lazy dog)

        • 4. Multiple sentences strung together: paragraph

      • Protein Structure

        • Primary: sequence of amino acids

          • What we get from reading genetic code

          • Doesn't say much abt protein

        • Secondary: repeated structures (alpha helix & beta sheet)

          • H-bond interactions between "backbone" of amino acids

          • 2 major structures form:

            • Alpha helix

            • Beta sheet

          • Tells us more abt shape/function than primary structure

        • Tertiary: 3D shape

          • Determined by actions between R-groups

          • Gives us 3D shape/function of the protein

        • Quaternary: several polypeptides interacting

          • Some proteins are made of multiple polypeptides

          • Interaction between polypeptides to form single protein = quaternary structure

    • Protein Functions:

      • Structure

      • Transport

      • Movement

      • Signaling/communication (including immune response)

      • Enzymes: Class of protein that catalyzes reaction

        • Catalyst: Molecule that lowers activation energy of reaction... not consumed in reaction

        • Typically named by adding "-ase" to what the enzyme acts on (ex: Lactase breaks down lactose)

        • Enzyme Function:

          • Enzymes act on a substrate

          • Reaction takes place @ active site

          • Enzymes are specific... tend to catalyze 1 and only 1 reaction

          • Lock and key model: Idea that only 1 type of molecule is shaped correctly to bind w/ active site

• Each has its own building blocks/distinctive properties

Cell Theory

• All organisms are made of 1 or more cells

• Cell is basic unit of living things

• All cells come from existing cells

What is a cell?

• Membrane-bound structure

• Contains all material necessary for life

• All cells

  • Have DNA

  • Have a cell membrane

  • Have sub-cellular structures

Why are cells small?

• Pretend cell is a cube (actually not a bad approximation)

• Surface area = square

• Volume = cube

• Cells absorb nutrients across their surface area, but use them in their entire volume

• Surface Area:Volume ratio

2 main types of cells

• Prokaryotic: archaea and bacteria

  • No membrane-bound organelles, incl. Nucleus

  • Always single-celled

  • Most diverse & numerous group

• Eukaryotic: animals, plants, fungi, etc.

  • Membrane-bound organelles incl. Nucleus

  • Single or multicellular

  • Complex cells, moderately diverse

Prokaryotic Cell Structure

• Cell membrane (all cells have one)

• Nucleoid region where DNA is found

• Many ribosomes that produce proteins

• Cell wall outside cell membrane; provides protection

• Capsule outside cell wall; provides protection & helps cell stick to things

• Plasmid: small circular bit of DNA carrying 1 to a few accessory genes

  • Not part of main chromosome

• Flagellum: whip-like extension for movement

• Fimbriae: extensions that help cell attach to things

• Pilus: for exchanging genetic info

Eukaryotic Cells

• Similarities with prokaryotes:

  • Cell membrane

  • DNA

  • Ribosomes

  • Cytoskeleton

  • Cell wall

  • Flagella

• Differences

  • Eukaryotes much bigger

  • Membrane-bound organelles

• Cell Membrane:

  • Phospholipid bilayer

  • Also contains

    • Proteins

    • Carbohydrates

    • Steroids (eg. cholesterol)

  • Fluid-mosaic model

    • Membrane = fluid, elements move around

    • Membrane composed of many diff parts

  • Roles:

    • Defines/delineates cell

    • Selectively permeable (controls entry/exit)

    • Communication w/ other cells

    • Receiving/responding to signals

    • Holding cell in place

• Nucleus

  • "Control center" of cell

  • Contains all cell's DNA

  • Structure:

    • Nuclear envelope: double membrane

    • Nuclear pores: allow/control entry and exit via pore complex

    • DNA contained in chromosomes, combined w/ protein to make chromatin

• Nucleolus

  • Sub-section of nucleus (not separate by membrane)

  • Dense region of DNA where ribosomes made

  • Combines rRNA w/ protein

• Cytoplasm

  • Broad: everything outside the nucleus, including organelles

  • Often used in place of cytosol, the fluid that makes up most of the cell

  • Most cellular activity occurs here

• Ribosomes

  • Made of rRNA & protein, no membrane

  • Make proteins

  • 2 subunits: large & small

  • 2 types

    • Free: float in cytoplasm, make proteins for use in cell

    • Bound: attached to Rough ER, make proteins for export

• Endomembrane System

  • Large complex of inter-related organelles that share an evolutionary origin

  • Carries out

    • Protein synthesis/modification/transport

    • Metabolism of lipids

    • Detoxification

  • Includes

    • Nuclear envelope

    • ER

    • Golgi

    • Lysosomes

    • Transport vesicles

• Endoplasmic Reticulum (ER)

  • Large network of membranes & compartments

  • 2 types w/ distinct function

    • Rough (RER)

      • Associated w/ ribosomes

      • Ribosomes make proteins & release them into ER

      • RER folds/modifies proteins

      • Proteins "tagged" for specific destinations

      • All secreted & most membrane-bound proteins travel thru RER

    • Smooth (SER)

      • Series of membrane-bound tubes

      • Production of lipids

      • Polysaccharide metabolism

      • Detoxification

      • Storage of calcium (in some cells)

• Golgi Apparatus

  • "Warehouse" or "shipping center"

  • Receives proteins from ER, prepares for export: adds sugar "tags"

  • Directionality

    • Cis side towards ER, receives transport vesicles

    • Trans side towards membrane, sends vesicles away

• Lysosomes

  • Small organelle filled w/ digestive enzymes (hydrolytic)

  • Roles

    • Breaks down polymers to harvest monomers

    • Breaks down old organelles for recycling

    • Digestion in unicellular organisms

    • Destruction of pathogens

    • Apoptosis

• Energy Conversion

  • Cells work w/ 2 main types of energy

    • Light

    • Chemical

  • 2 main "currencies"

    • ATP

    • Sugars

  • Cells must be able to convert between energy forms

• Mitochondria

  • Conversion of sugar energy to ATP energy

  • 2 membranes, inner membrane folded into numerous cristae

  • Site of Krebs cycle & electron transport chain

  • Contains DNA

• Chloroplasts

  • Found in plant & algal cells

  • Conversion of light energy to chemical energy

  • 3 membranes, innermost contains chlorophyll

  • Contains DNA

• Endosymbiosis

  • Chloroplasts & mitochondria originated as individual cells

  • Ancestral eukaryote engulfed prokaryote, but developed symbiotic relationship

    • The eukaryote ate the prokaryotic chloroplast/mitochondria, but instead of consuming it, the mitochondria/chloroplast lived inside the eukaryote

  • Evidence:

    • Presence of DNA

    • Presence of prokaryotic ribosomes

    • Prokaryotic double membrane

• Structural Organelles

  • Cytoskeleton

  • Centrosomes

  • Cell wall

• Cytoskeleton

  • Network of protein fibers throughout the cell

  • Gives cell shape, organizes contents

  • 3 components

    • Microfilaments (smallest)

    • Intermediate filaments (medium)

    • Microtubules (biggest)

      • Similar structure to flagella/cilia

• Centrosomes

  • Animal cells only

  • Contains 2 centrioles

  • Organizes cell division

• Cell Wall

  • Plant, algae, fungi cells

  • Rigid structure outside cell membrane

  • Provides structural support & protection

  • Contains openings: plasmodesmata

Diffusion

• Particles = always in motion

• What happens if they all move around randomly?

• Diffusion: movement from high to low concentration

Osmosis

• What if smth can't diffuse?

• Reminder: large and/or polar molecules can't cross cell membrane

• Water can move thru aquaporins

• Osmosis: movement of water across a membrane from low solute concentration to high solute concentration

• Hypertonic: more concentrated solution when comparing 2

• Hypotonic: more dilute solution when comparing 2

• Isotonic: solution w/ same amt. concentration when comparing 2

• Osmotic Pressure:

  • Cells are filled w/:

    • Salts

    • Sugar

    • Proteins

  • Almost always hypertonic to fresh water

Facilitated Diffusion

• The movement of specific molecules across cell membranes thru membrane proteins

• When diffusion would take too long/be impossible

• Hundreds of diff proteins exist

• Active Transport

  • Moves materials against concentration gradient

  • Only 1 direction

  • Requires energy (ATP: Adenosine Triphosphate) bc either pushing smth against concentration gradient or pushing smth big

  • 2 types: Molecular & Endocytosis

  • Molecular Active Transport

    • Small molecules & ions

    • Allows concentration of substances in a particular location

    • Ion pumps

  • Endocytosis & Exocytosis

    • Large molecules & even solid clumps of materials

    • Endocytosis: Material engulfed by cell thru pockets of cell membrane

    • Pocket eventually forms vesicle in cytoplasm

    • Phagocytosis

      • Large particles

      • Extensions of cytoplasm surrounds & engulfs particle

      • Requires considerable amt of energy

      • Type of endocytosis

    • Pinocytosis: Tiny pockets form along cell membrane, fill w/ liquid, & pinch off to form vesicles in cell

    • Exocytosis: vesicle membrane fuses w/ cell membrane, forcing its contents out of the cell

      • Many cells also release large amts of materials from the cell

Terminology

• Metabolism: sum of all reactions occuring in cell

  • Catabolic: breaking down

  • Anabolic: building up

• Autotroph: organism capable of carbon fixation

• Heterotroph: organism incapable of carbon fixation

• Carbon fixation: inorganic carbon -> organic carbon

Energy

• Comes in many forms

• 2 main forms cells use

  • Chemical

  • Light

• 2 main "currencies"

  • Glucose: long term, stable

  • ATP: shorter term, easy to break

• ATP:

  • 3 parts

    • Adenosine

    • Ribose

    • 3 phosphates

  • Energy stored in bonds

  • ATP & Energy:

    • ATP uses centers around phosphates

    • Hydrolysis ... cuts off final phosphate, yielding ADP and energy

    • ADP: Adenosine Diphosphate

    • Condensation reaction ... adds phosphate & energy ... "charges" ATP

  • Bonds & Energy

    • Breaking bonds takes energy

    • Hydrolysis of ATP releases energy

    • Electrons

      • Phosphates are dense in electrons

      • Electrons repel each other

      • Electrons in ATP are in high energy state

      • After hydrolysis, electron returns to lower energy state, releases energy

  • Energy cannot be created nor destroyed

  • Metabolism is all abt energy transfer to do work

    • Chemical work, eg. digestion

    • Mechanical work, eg. movement

    • Transport work, eg. ion pumps

    • Coupling: endergonic work (requires energy) coupled to exergonic reaction (ATP hydrolysis)

    • About 99% of energy comes from sun

    • Overall metabolism: harvest energy from photons, transfer (via intermediates) to do work

  • Intermediates

    • Glucose

    • ATP

    • NAD+ / NADH ... FAD / FADH2

      • Mobile electron carriers

      • Assist in transfer of energy

    • NADP+ / NADPH in plants

Cellular Respiration

• Aerobic cellular respiration has 3 stages

  • Glycolysis (anaerobic)

  • Krebs cycle/citric acid cycle (aerobic)

  • Electron transport chain (aerobic)

• Aerobic = requires oxygen; anaerobic = does not require oxygen

• Location (in eukaryotes)

  • Glycolysis in cytosol

  • Krebs cycle and Electron transport chain in mitochondria

What to keep track of:

• For each stage:

  • Where it takes place and if it needs oxygen

  • What goes in (type & number)

  • What comes out (type & number)

  • Most bookkeeping is "per glucose"

• Ask...

  • What happens to the carbon?

  • What electron carriers are involved?

  • Do we get or spend ATP?

Stage 1: Glycolysis

• Glyco = sugar, lysis = splitting

• 1 glucose split into 2 pyruvate

• Inputs: Sugar, ATP, NAD+

• Outputs: ATP, NADH

• Glucose breakdown

  • Glucose is overall source of energy, but bonds need to be broken

  • Initial phase requires 2 ATP

  • Adds phosphates

  • Destabilizes carbon-carbon bonds

  • Energy-dense electrons harvested, breaks bonds to yield 2 pyruvates

  • Additional electrons will be harvested in citric acid cycle

• ATP Production

  • Glucose breakdown lowers free energy... the products have lost energy

  • Energy has to go somewhere

  • Energy is used to "charge" 4 ATP

  • Net gain of 2 ATP

• NADH Production

  • Some free energy transferred to make ATP

  • Some free energy transferred in form of electrons

  • 2 NAD+ EACH are reduced w/ 2 electrons, yields 2 NADH

  • Electrons hold energy; will be used in electron transport chain

• Inputs

  • 1 Glucose

  • 2 NAD+

  • 2 ATP

  • 2 ADP (usually ignored)

• Outputs

  • 2 pyruvate

  • 2 NADH

  • 4 ATP (for a NET gain of 2)

• Net gain: 2 pyruvate, 2 NADH, 2 ATP

Getting Ready for Krebs

• At end of glycolysis, we have 2 pyruvate

• Pyruvate still contains a lot of energy'

• Pyruvate Oxidation: precursor step to Krebs cycle

  • Each pyruvate oxidized w/ acetate, combined w/ CoA (coenzyme A) to make acetyl-CoA

  • 1 NAD+ reduced to NADH (2 total)

  • 1CO2 produced (2 total)

Citric Acid Cycle (Overview)

• 8-step cycle for harvesting electrons

• Runs once per pyruvate (2x per glucose)

• By end:

  • Glucose completely oxidized

  • High-energy electrons transferred

  • Some energy (ATP) created

• Citric Acid Cycle (Carbon)

  • Carbon enters cycle as 2 acetyl-CoA

  • CoA "drops off" 2 carbons... combines w/ oxaloacetate to form citric acid

  • Over series of steps, carbon oxidized

    • Electrons transferred to form NADH

    • Oxidized CO2 released

  • Oxaloacetate regenerated to restart cycle

• Citric Acid Cycle (Electrons)

  • If carbon is oxidized, smth must be reduced

  • High-energy electrons transferred to electron carriers

    • 3 NADH per cycle

    • 1 FADH2 per cycle

  • These electron carriers will return in ETC

• Citric Acid Cycle (Energy)

  • Overall, CAC doesn't produce much free energy

  • Most energy will be used in ETC

  • Small amt used to make single ATP per cycle

Products (per glucose)

• Pyruvate oxidation:

  • 2 NADH

  • 2 CO2

• Krebs cycle:

  • 6 NADH

  • 2 FADH2

  • 4 CO2

  • 2 ATP

• Grand total (everything so far)

  • 10 NADH

  • 2 FADH2

  • 6 CO2

  • 4 ATP

Electron Transport Chain (Overview)

Electron Transfer

• NADH and FADH2 holding high-energy electrons

• ETC starts w/ transfer of e- to ETC protein complexes

• Electron carriers oxidized back to NAD+ and FAD

• Oxidized electron carriers return to glycolysis/Krebs cycle

Using Electrons

• As electrons travel thru ETC they transition from high to low energy

• Reminder: energy must go somewhere

• Energy used to do work: pump hydrogen ions across membrane

• Forms proton gradient

Fate of the Electrons

• At end of ETC, electrons have lost most of their energy

• What has been pulling them thru the chain?

• Oxygen: highly electronegative, attracts electrons

• At end of chain, oxygen is reduced, reacts with hydrogen to form water

• Without oxygen, nothing to pull electrons through chain

Protons & ATP

• Action of ETC proteins leads to proton gradient

• High concentration of H+ in intermembrane space

• Protons wanna flow back into matrix

• 1 way back: ATP synthase

ATP Synthase

• Large, complex protein embedded in inner membrane

• Contains channel allowing proton flow

• Proton flow causes enzyme to spin

• Energy of spinning used to catalyze ATP formation

• Oxidative phosphorylation

ATP Formation

• Hydrogens flowing down concentration gradient provide energy for ATP formation

• At maximum, respiration leads to formation of 36-38 ATP per glucose

• In reality, closer to 30 net ATP per glucose

  • Leaky membranes

  • Some energy spent moving things into mitochondrial matrix

Glycolysis, oxygen, & ATP

• Observation 1: glycolysis is anaerobic process

• Observation 2: if ETC stops, glycolysis will also stop

NADH oxidation

• If the ETC stops, NADH will not be oxidized back into NAD+

• NAD+ is oxidizing agent in glycolysis

• W/out NAD+, nothing to keep glycolysis going

• Fermentation: process of allowing NADH to allow additional glycolysis

  • Caveat: fermentation does NOT generate ATP

  • Step after glycolysis to regenerate NAD+ in anaerobic conditions

  • 2 types:

    • Lactic acid fermentation

      • After glycolysis, pyruvate can be reduced instead of oxidized

      • 1 way: react w/ NADH, picks up e-s (and hydrogen) to become lactate

      • NAD+ regenerated for glycolysis

      • Lactate = waste product

      • source of burning sensation in intense exercise

    • Alcohol/ethanol fermentation

      • Another form of regenerating NAD+

      • 2-step process

      • Produces CO2 and ethanol

      • Commercially important

        • Alcohols (ex: beer, wine)

        • Bread (CO2 makes bread rise)

        • Fermented vegetables (ex: sauerkraut, kimchi)

        • Yogurts

        • Some condiments (ex: soy sauce)

Overall Recap

• Glucose has been completely oxidized (stripped of high energy electrons)

• Some energy used to make ATP

• Most energy used to power ETC, via NADH & FADH2

• ETC creates proton gradient that powers ATP synthase

• Roughly 30 ATP generated per molecule of glucose

Intro

• Photosynthesis: conversion of light energy to chemical energy

• Inputs: light & water

• Outputs: glucose

• Carbon reduced using energy harvested from photons (opposite of cellular respiration)

Equation:

6CO2 + 6H2O + energy -> C6H12O6 + 6O2

Photosynthesis Overview:

• 2 parts: Light-independent & light-dependent reactions

• Light-dependent reactions (LDR):

  • Harvest light energy to energize electrons

  • Electrons used to pump hydrogens and reduce NADP+

  • Creates ATP & NADPH

• Light-independent reactions (LIR)

  • Also called Calvin cycle or dark reactions

  • Uses energy from ATP & NADPH to reduce carbon

  • End product: useable carbon

  • Carbon fixation

Light, Energy, & Pigments

• Light form of electromagnetic energy

• Basic unit: photon

• All photons carry energy

  • Shorter wavelength = higher energy

• Light absorbed by pigments

• Chlorophyll: primary photosynthetic pigment

  • Absorbs primarily red & blue light

  • Assisted by accessory pigments

  • Comes in many forms (a, b, c, d, e, & f so far)

  • Arranged in light-harvesting complexes like solar panels

  • Works by absorbing photon, using energy to excite electron

    • Excited electron is at higher energy level

    • Chlorophyll passes electron to other molecules, becomes oxidized

    • Electrons will function much like those in ETC of respiration

Chloroplasts

• All of photosynthesis takes place in chloroplasts

• Structure:

  • Triple membrane

  • Innermost membrane: thylakoid stacked into grana

    • Site of chlorophyll

• Lumen: innermost space in thylakoids

• Stroma: space between thylakoid & inner membrane

• LDR occur across thylakoid membrane

• LIR occur in stroma

Photosynthesis part 1

• 1st part of photosynthesis: light-dependent reactions

• Inputs: water & light

• Outputs: oxygen (waste), ATP, NADPH

• Overall process:

  • Photon excites electron, energy used to do work

  • Excited electron replaced w/ electron from water

  • ETC: proton pumps create proton gradient

  • ATP synthase harvests proton gradient to make ATP

  • Electron used to reduce NADP+ to NADPH

Light-Dependent Reactions: Harvesting Light

• Process starts w/ chlorophylls absorbing photons in Photosystem II (PSII)

• Charged electrons passed to electron transport proteins

• Chlorophyll now down an electron, regains it from water

• Water is oxidized, creating hydrogen & oxygen

• Source of the oxygen gas we breathe

Light-Dependent Reactions: Electron Transport

• Excited electrons contain energy, can be used to do work

• Pass thru ETC, go from high to low energy

• Energy has to go somewhere

• Proton pumps create proton gradient

• Functionally just like ETC in cell respiration

Light-Dependent Reactions: Harvesting More Light

• While ETC is happening, Photosystem I (PSI) also absorbing light

• Excited chlorophyll passes electron to 2 possible destinations

  • Back to ETC

  • NADP+ to make NADPH

• Destination of electron depends on needs for ATP vs NADPH

• Lost electron replaced w/ low-energy electron leaving ETC

Light-Dependent Reactions: Summary

• Light harvested to energize electrons in PSII

• Electrons used to do work: pump protons

• Electrons eventually recharged in PSI, can do more work or be transferred to make NADPH

• Electrons lost from chlorophyll replaced with electrons from water; creates oxygen

• Protons pumped by electrons flow thru ATP synthase to make ATP

• Overall products: oxygen, ATP, NADPH

  • Oxygen = waste

  • ATP & NADPH will be used in Calvin cycle

Photosynthesis Part II: the Calvin cycle

• LDR converts light energy to chemical energy

• LIR converts short-term chemical energy to longer-term storage

• Occurs in stroma

• Summary: uses chemical energy from LDR to fix and reduce carbon

Calvin Cycle: Summary

• Aka light-independent reactions, dark reactions, etc.

• Do not directly depend on light

• Inputs:

  • CO2

  • NADPH

  • ATP

• Main product: sugar

• 3 phases

  • Carbon fixation

  • Sugar reduction

  • Regeneration of RuBP

Calvin Cycle: Carbon Fixation

• Cycle starts w/ addition of carbon to 5-carbon sugar called ribulose biphosphate (RuBP)

• Performed by enzyme called ribulose-1, 5-biphosphate carboxylase-oxygenase aka RuBisCo

• Each reaction represents 1 new fixed atom of carbon (so a glucose requires 6 turns of the cycle)

Calvin Cycle: Sugar Reduction

• Remember: glucose is a reduced form of carbon

• To hold energy, carbon must gain electrons/be reduced

• Phase 2 of Calvin Cycle reacts NADPH and ATP with sugar to transfer high-energy electrons

• Eventual product after 3 cycles: 1 glyceraldehyde-3-phosphate (G3P)

Calvin Cycle: Regeneration of RuBP

• Reminder: cycles end w/ starting material

• Remaining carbons will be rearranged to regenerate original RuBP

• Requires spending some ATP

• Overall, for every 1 G3P produced, 5 3-carbon sugars are rearranged into 3 5-carbon RuBP

Water & Gas

• Plants in arid places can have multiple adaptations

• 1 adaptation: closing stomata

• Pro: no losing water

• Con: no exchanging gases

• RuBisCo

  • Carboxylase-oxygenase

  • If there's too much oxygen sugars get oxidized, not reduced

Helping Rubisco

• RuBisCo can react w/ oxygen or CO2

• Problem: oxygen and CO2 build up relative to each other

• Can be solved by separating LDR. & LIR

• 2 ways:

  • C4 plants: separate reactions spatially

  • CAM plants: separate reactions temporally

C4 Pathway

• Way to separate oxygen production & carbon fixation

• 2 distinct parts of leaves

  • Mesophyll cells: LDR and initial carbon fixation

  • Bundle-sheath cells: Calvin Cycle

• Carbon is fixed TWICE

  • 1st in mesophyll by PEP carboxylase

  • Carried by oxaloacetate to bundle

  • Second time in bundle-sheath by Rubisco

  • CO2 is concentrated near Rubisco, increases efficiency

CAM pathway

• Crassulacean Acid Metabolism

• Carbon also fixed twice

  • Stomata open at night, carbon fixed as malic acid, stored in vacuoles

  • Respiration lowers oxygen levels

  • During day, stomata closed, carbon released from malic acid for Calvin cycle

• Fixation reactions separated over time

• Less efficient, but better at saving water

Controls on Photosynthesis

• Water availability, but usually not limiting

• CO2 availability

• Light

• Temperature