BIOL 111 Exam 2

Membranes

• A “collage” of different proteins embedded in the fluid matrix of the lipid bilayer

  • Abstract 

  • Each individual pieces don't make sense by themselves but works when put together

• Flexible but maintains structure

Plasma membrane

• Dynamic and ever-changing boundary that separates the living cell from its nonliving surroundings

• Exhibits “selective permeability”

  • Allows some substances to cross more easily

  • Ex: bouncer at a nightclub

    • Certain people in

    • Stop certain people

• Functions to:

  • Define outer border of cells and organelles

  • Manages what enters and exits: “bounder” of the cell

  • Receives external signals and initiates cellular responses

  • Adheres to neighboring cells

Fluid mosaic model

• Membrane is a fluid structure with a “mosaic” of various components embedded in it

  • Mixture of phospholipids, cholesterol, proteins, and carbs

• Glycolipid and glycoprotein

• Phospholipid: main component

  • Phospholipid bilayer

• Protein go from external environment to internal environment

Phospholipids

• Major component of plasma membrane

• Amphipathic → contain both hydrophilic and hydrophobic regions

  • Head: loves water

  • Tails: hates water

• Can move around within the bilayer

  • Movement makes it impossible to form a completely impenetrable barrier

  • Allow for changing environment

Fluidity of the membrane (Temperature)

• Temperature → affect movement “rate” and distance

  • Iceberg in ocean

  • Colder = closer to phospholipids → restricts small molecules

    • Rigid; may break

  • Warmer = more separated phospholipids → leaves larger gaps

    • More flexible

    • May not hold the shape

Fluidity of the membrane (Cholesterol)

• Cholesterol → randomly distributed across the bilayer, helping it stay fluid

  • Introduce some gaps

  • Increased fluidity at low temperatures and decreases fluidity at high temperature

    • More cholesterol at low temp

    • Less cholesterol at high temp

  • Acts as a buffer: keeps membranes fluid when cold and not too fluid when hot

    • Fix rigidity

Fluidity of the membrane (Fatty Acid)

• Fatty acid composition → make up the hydrophobic phospholipid tails

  • Saturated fats are straight, easy to pack tight

    • Hot → increase saturated fat

  • Unsaturated fats have double bonds that create kinks in the chains, making it more fluid

    • Cold → increase unsaturated fat

  • Counterbalance swings in temperature

Proteins

• Second major component of membranes

• Functions include: transportation, receptors, enzymatic, binding

  • Ex: tollway 

• Integral proteins: span the entire bilayer moving things in/out

• Peripheral proteins: either on exterior or interior surface 

  • Usually enzymes or structural attachments

  • Don’t span both pieces of bilayer

Carbohydrates

• Third major component of membranes

• Only located on exterior surface of the plasma membrane and bound to something else

  • Bound to protein → glycoprotein

  • Bound to lipid → glycolipid

• Function in cell-to-cell recognition and attachment

• Viral entry mechanism → how virus gets into body/how we can stop viruses from entering body

Receptor proteins and viral entry

• Most viruses use a glycoprotein called viral receptors to attach to a host cell

  • To get into body

• HIV has gp 120 → looks for “glycoprotein 120” that adheres to human immune cells CD4 receptor

• CD4: cell adhesion molecule that functions to keep other immune cells close by when immune response is generated

• Same way find way in → same way to develop vaccines to keep them out

• Lock and key mechanism

Asymmetric membrane

• Plasma membranes are asymmetric as the inner surface differs from the outer surface

  • Interior is NOT identical to exterior

• Examples:

  • Interior proteins anchor fibers of the cytoskeleton to the membrane

    • Inside cytoplasm anchor fibers to cytoskeleton

  • Exterior proteins bind to the extracellular matrix

  • Glycoproteins bind to the substances the cells need to import

• Membranes have distinct inside and outside faces

  • Affects the movement of proteins synthesized in the endomembrane system

Endomembrane system

• Group of membranes and organelles that work together to synthesize, modify, package, and transport proteins and lipids out using the:

  • Endoplasmic reticulum (ER)

  • Golgi apparatus

  • Nuclear envelope

  • Plasma membrane

  • Lysosomes

• Ribosome → endoplasmic reticulum → golgi apparatus → golgi vesicle

  • Make protein → fold and modify protein → sort and package protein → transport protein to target destination

• Membrane structure results in selective permeability

  • Works to keep things separated

  • A cell must exchange materials with its surroundings

    • A process controlled by the plasma membrane

Permeability of the lipid bilayer

• Membranes are selective barriers

• Smaller and nonpolar → easier to cross membrane

  • Size

  • Membrane is also nonpolar

    • Like dissolves like

• Small, nonpolar molecules: can pass easily and quickly through and do not require proteins for transport

  • O2 and CO2

• Small, polar molecules: more difficult than nonpolar; hydrophobic tails of the bilayer make it tougher and slower, but they can cross without the help of proteins

  • Ex: H2O

• Large, nonpolar molecules: can pass through but it is also a slow process

  • Ex: carbon rings, glucose, nucleotides, amino acids

• Large, polar molecules and ions: size and charge make it too difficult to pass through the nonpolar region of the phospholipid membrane without help

  • Ex: simple sugars and H+ ions

Transport across the plasma membrane

• Cells must allow material to enter and exit

• Permeability of the membrane allows cytosol (inside the cell) solutions to differ from extracellular (outside the cell) fluids (asymmetrical membrane)

Diffusion

• Passive transport of any solute moving from areas of high concentration to areas of low concentration

  • Substances move down a concentration gradient

  • Ex: mix food coloring in water

Osmosis

• Special type of diffusion!

• Focus on the movement of water across a semipermeable membrane

  • Determined by solute concentration → things dissolved in the water

• Water moves from areas of low solute concentration to areas with a higher solute concentration

• Differences in water concentration occur when a solute cannot pass through the membrane

• Adding more water into areas with a lot of solute

High blood pressure

reduce sodium intake 

• Salt sucks

• More sodium → more blood volume increase → harder heart has to work

Water potential

• Tendency of water to move from one place to another

• Remember, water will move from areas of high solute concentration to areas of low solute concentration

• Know Hypo and Hypertonic solutions

• Animal cells → pressure required to stop the net movement of water

  • Hypertonic: cell can shrink

  • Hypotonic: cell can burst

  • Isotonic: ideal for animal cells

• Plant cells → positive pressure caused by movement of water into a cell

  • Don't like isotonic situations

  • Prefer being in a hypotonic condition

    • Grocery store: spray water onto vegetables

    • Don't burst because they have a cell wall

  • Hypertonic situation: shrink

Tonicity

• Ability of a solution to cause a cell to gain or lose water

  • Changes the volume in the cell by osmosis

  • Has great impact on cells without cell walls

  • Three different conditions

    • Isotonic

    • Hypotonic

    • Hypertonic

• Animals and other organisms without rigid cell walls:

  • Live in hypertonic and hypotonic environments

  • Prefer isotonic

Isotonic solution

• Concentration of solutes 

  • Same inside and outside of the cells

  • Equilibrium

• No net movement of water

  • Water flows both directions at an equal rate

Hypotonic solution

• Concentration of solutes

  • Less outside in the solution than in the cell

    • Hypertonic cell

• Cell will take in water

• Hypo → under, beneath, less

  • Hypoglycemia → low blood glucose

    • Beneath normal level

Hypertonic solution

• Concentration of solutes 

  • Greater outside in the solution than in the cell

• Cell will lose water

• Hyper → over, excess, more

  • Hyperthyroid → too much thyroxine produced

    • Over the normal level

• Normally put cell in salt water solution

Water balance of cells with walls (plants)

• Cell walls: help maintain water balance

• Plant cells are turgid/firm and generally healthiest in a hypotonic environment

  • Ideal situation

Osmoregulation by other organisms

• Freshwater protists like paramecia and amoebas use contractile vacuoles which pumps water out of the cell to prevent bursting

• Marine invertebrates have internal salt concentrations that match their environment

• Fish excrete diluted urine which gets rid of excess H2O or salts

• Osmoreceptors in the brain cells monitor solute concentrations in our blood

  • Releases hormones that affect kidney function

Passive transport → facilitated diffusion

• No use of energy

• Moves substances down their concentration gradients (high → low concentration)

  • Requires the use of transmembrane proteins:

    • Channel proteins 

    • Carrier proteins

    • Span bilayer completely

• Ions and large polar molecules use this for diffusion

Channel proteins

• Transmembrane, completely spanning the membrane

  • Completely penetrate hydrophobic core of lipid bilayer

• Some open all the time

• Others are gated

  • Only open when a signal is received

  • Some only allow small molecules to pass through; larger molecules are too big to fit through the channel

  • Other channels are affected by charge

    • Attract positive ions; repel negative ions

    • Attract negative ions; repel positive ions

• Only “appropriate” molecules pass into and out of the cell:

  • Size of molecule

  • Charge of molecule

Examples of channel proteins

• Insulin receptor is a transmembrane receptor that is activated by insulin

• Metabolically, the insulin receptor plays a key role in the regulation of glucose homeostasis

• Lock and key 

  • Insulin receptor open → need to start taking glucose out of bloodstream and to other parts of body

  • Won't let other things sneak in

• Scorpion venom contains chlorotoxin which can block channels in muscle cells that let chloride ions in and out

  • These ions normally help tell muscle cells when to relax

    • Paralyze victim 

    • When channels get blocked, all the muscles flex at once leaving the animal tensed up and unable to move

• Aquaporins are water channels

  • Transfer large quantities of water molecules across the hydrophobic plasma membrane

• Kidney function and vision for animals

• Water and nutrient movement; metal detoxification for plants

Carrier proteins (Passive)

• Specific to a single substance

  • Binds to that substance 

  • Changes shape

  • Carries it to the other side

• Many allow movement in either direction

  • As concentration gradients change

• Example: glucose transport proteins or “GLUTS”

  • Bloodstream to cells

  • All phyla of life have GLUTS

    • Very important

Main differences between Channel and Carrier Proteins

• Protein channel

  • Open most of the time

  • Passage of molecules from outside in/inside out

• Carrier proteins

  • More specific

  • Change conformation of protein molecule

Active transport across the plasma membrane

• Must be against its concentration gradient (from low to high concentration)

  • Can also move ions against their electrochemical gradient

    • Like H+ ions to a solution that is more positive

• Energy is ALWAYS required

  • Usually in the form of ATP (primary and bulk)

  • Atp powers process by shifting a phosphate group

    • From atp to the transport protein

    • Induces a conformational change of the protein

    • Then translocates the solute across the membrane

• Energy source can also be an electrochemical gradient (secondary)

  • Produced as a product of primary active transport

Carrier proteins (Active)

• Active transport can occur through transmembrane, integral carrier proteins called “pumps” and there are 3 types

  • Uniporters: carry 1 molecule or ion

  • Symporters: carry 2 different molecules or ions in the same direction

  • Antiporters: carry 3 different molecules or ions in different directions

Primary active transport

• Moves an ion or molecule up/against its concentration gradient (from low to high)

  • Uses energy from atp hydrolysis

  • Always start with atp

• Example: sodium-potassium pump

  • Moves 3 Na+ out of cell for every 2 K+ into cell using 1 atp

  • Primary example of active transport

  • Regulates nearly everything in out body

  • Maintain resting, heart beat, fire neurons, etc.

• Hydrolysis of atp → adp allows for energy to transport ions across membrane

ATP hydrolysis “powers” secondary active transport

• Electrochemical gradients: result from the combined effects of concentration and electrical gradients

  • Differential charges

  • Movement because moving from negative to positive/positive to negative

  • Movement caused by the gradient of ions across a membrane

    • Different charges across the membrane

  • Cytoplasm contains more negatively charged molecules (ions and proteins) than the extracellular fluid (fluid outside cell)

• Electrogenic pumps: transport proteins, generates voltage across a membrane 

  • Membrane potential → voltage difference across a membrane 

    • Between in vs out

    • Important in the maintenance and functioning of our nervous system

• Potassium chloride

  • Affects charge → stops the heart

  • Eliminates concentration gradient

  • Flooding heart with potassium

Secondary active transport

• Moves an ion or molecule up/against its concentration gradient (low to high concentration)

  • Energy source not ATP→ electrochemical gradient

• Many amino acids and glucose enter the cell in this way

Bulk transport

• When cells need to import/export molecules/particles that are too large to pass through a transport protein

  • Large proteins or macro molecules

• Endocytosis (importing)

• Exocytosis (exporting)

Exocytosis

• Outside of cellular process

• Transport vesicles containing substances to be secreted fuse with the plasma membrane

  • Contents are then released outside of the cell into the extracellular fluid

  • Main function of the endomembrane system

Endocytosis

• Into cellular process

• Forming vesicles from plasma membrane and bring molecules INTO the cells for various functions

• 3 main methods

  • Phagocytosis

    • Eating 

    • Solid particle encapsulated by forming vesicle

  • Pinocytosis

    • Fluid and aqueous particles

    • Cellular process of drinking

    • Ladle of soup into a bowl

  • Receptor mediated endocytosis

    • Very specific means of entry into cell

    • Receptor molecules that only take in substances that fit

Metabolism

• Defined as the totality of an organism’s chemical reactions

  • Really complex

• An organism’s metabolism:

  • Transforms matter and energy

  • Is subjected to the laws of physics

• Amino acids take up space and have mass

Metabolic pathways

• Consists of thousands of biochemical reactions that all require energy transformations

• Many steps required and each step:

  • Is a separate chemical reaction

  • Catalyzed by a specific enzyme

• End result is a “product”

• Two types of pathways required to maintain the cell’s energy balance:

  • Catabolic 

  • Anabolic 

Example of metabolic pathway

• Tyrosine is an AA that undergoes a series of reactions to make adrenaline (epinephrine) as a product

  • Fight or flight

• Along the way, dopamine is synthesized at an intermediate step

Catabolic pathways

catabolism

• Break down complex molecules into simpler ones

  • Ex: why you eat food

• Release energy

• Best example in biology: cellular respiration, the breakdown of glucose molecules

• Large molecules are broken down into smaller ones → energy is released

Catabolic

• Process: breaks down molecules

  • Polymer → monomer

• Energy: released; exergonic

• Delta G: negative

  • Spontaneous

• Stability: more stable

• Example: respiration; hydrolysis of ATP to ADP

Anabolic pathways

• Build more complex molecules

• Require energy

• Top example in biology is photosynthesis

• Small molecules are assembled into large ones → energy is required

• Example: photosynthesis

• Anabolic

  • Builds up molecules

    • Monomer → polymer

  • Energy: required; endergonic

  • Delta G: positive; non-spontaneous

  • Stability: less stable

  • Example: photosynthesis; synthesis of ATP to ADP

Energy

• Capacity to cause change

  • Exist to perform work

• Exists in various 

  • Fundamental to all metabolic processes

  • Rearrange matter form one form to another

• Sustains most of earth’s life

  • Comes from the sun

• Bioenergetics 

  • Study of energy flow through a living system

Types of energy

• Potential energy: stored energy, the energy matter has because of its structure

  • Membrane potential

    • Na+ moving in/out of cell

  • Chemical energy stored in molecular structures

    • Like in glucose molecules

  • In a compressed spring

  • Can use if change is made to thing holding energy

• Kinetic energy: energy in motion, movement of objects

  • Thermal energy: associated with the random movement of atoms or molecules

    • Heat: when thermal energy is transferred from one molecule to another

• Energy can be converted from one form to another

Additional energy types

• Free energy is similar to potential energy in that it describes the energy available to do work

  • Usable energy

  • A living system’s free energy: energy that can do work under cellular conditions

• Gibbs free energy (G)

  • The free energy change of a reaction

    • Determines whether a reaction is spontaneous or nonspontaneous

  • G is affected by all chemical reactions/biological processes

    • After a reaction the change is denoted as delta G

Free energy

• During a spontaneous change

  • Addition of external energy is NOT required

  • Free energy decreases and the stability of a system increases

• Delta G is negative (look at slide)

  • This happens when energy is released in a chemical reaction

• Example: creation of diamonds

• An exergonic/spontaneous reaction: energy is exiting the system

  • Proceeds with a net release of free energy (negative delta G)

  • Net release of free energy to take reactants and create products

• An endergonic/nonspontaneous reaction: energy is entering the system

  • Reactions that absorbs free energy from its surroundings

    • Delta G is positive

  • Smaller reactants/less free energy → take energy into system → make products excess of what we started out with

Activation energy

• Initial energy required for a reaction to proceed/start

• Heat energy from the surroundings is the main source in the cell

  • Usually obtained from the surroundings of the system

  • Helps reactants reach their transition state

    • Causes reactions to become contorted and unstable

      • Allows bonds to be broken or made

      • Once in this state, the reaction occurs very quickly

• Enzymes function by lowering the Ea barrier, delta G is unaffected

  • Lowers activation energy

  • Reduce energy required to do reaction

  • Don't necessarily start the reaction; make reaction easier to begin

Thermodynamics

• Study of energy transformations

• The term system indicates the matter under study and the surroundings are everything outside the system

  • A closed system is isolated from its surroundings

    • Reactions in a closed system eventually reach equilibrium where delta G=0

    • Can’t put things in; can't take things out

    • Ex: saucepan with lid

  • An open system energy and matter can be transferred between the system and surroundings

    • Organisms are open systems

    • Constant flow of food in and waste out

    • Prevents equilibrium → G never = 0

    • Ex: saucepan without lid

• Closed hydroelectric system

  • Water flowing downhill turns turbine that drives a generator providing electricity to a light bulb, but only until the system reaches equilibrium

  • Then becomes equal: turbine will not spin and light bulb will not work

• Open hydroelectric system

  • Constant flow of water into tank

  • Opening out of the tank

  • Constantly putting water in and rushing water out

  • Constantly spinning turbine

Laws of thermodynamics

• 1st law of thermodynamics

  • Energy can NOT be created or destroyed

  • Energy CAN be transferred and transformed

• 2nd law of thermodynamics

  • Spontaneous changes (do not require outside energy) increase the entropy/disorder of the universe

    • Why organisms can’t simply recycle energy

Biological order and disorder

• Biological systems are complex and highly ordered

• Entropy: chaos/disorder

• Entropy at the molecular level (overall trends, there are exceptions):

  • Entropy of a liquid state is greater than entropy of a solid state

  • Entropy increases when a substance is broken down into parts

  • Entropy increases as temperature increases

  • Entropy increases in reactions where the number of product molecules is greater than the number of reactant molecules

• According to the second law of thermodynamics, entropy increases whenever something happens

• Entropy → dispersal of energy

• Natural tendency of a system and humans is for entropy to increase

How is order created and maintained in biological systems despite ever increasing entropy (disorder)?

• Energy

  • Cells use a lot of energy to create and maintain order

  • Second law still holds true, entropy in the surroundings increases, largely due to the release of heat (also energy)

    • Internal cell maintain energy because of the use of energy

ATP: Adenosine Triphosphate

• Cell’s primary energy shuttle

  • Energy $$

• Powers cellular work by coupling exergonic and endergonic reactions

  • Back and forth changing 

• Chemical, mechanical, and transport work

ATP Structure

• Composed of an adenosine backbone + 3 phosphate groups attached

• Adenine attached to ribose with phosphate tail

  • Tail has 3 phosphate (tri=3)

• Broken down to ADP, accompanied by the release of energy

  • Break connection between two phosphates

  • Three phosphate → two

    • Adenosine diphosphate (ADP)

ATP hydrolysis: phosphorylation

• Energy is released from ATP when a phosphate bond is broken

  • Anytime we do something to a phosphate group

• ATP drives endergonic reactions by phosphorylation, transferring a phosphate to other molecules

• ATP hydrolysis is reversible

• Example: Sodium potassium pump

  • Main source of active transport

  • Using ATP and phosphorylation with ADP

• Think of it as a battery

Energy coupling

• Energy coupling: transfer of energy from catabolism to anabolism

  • Or the transfer of energy from exergonic processes to endergonic processes

  • Shifting back and forth between point A and point B

• Example: photosynthesis and cellular respiration

• Charged battery → hydrolysis reaction has energy released into anabolic/endergonic reactions

  • Energy-consuming processes

• Dead battery → take single organic phosphate and undergo another organic reaction

  • Remove water molecule: dehydration synthesis; reattaching inorganic phosphate back to ADP and regenerate ATP molecule

  • Energy is form of catabolic/exergonic fractions

    • Energy releasing process

• Spend money to earn money

• Both processes → process of phosphorylation

  • Messing around with phosphate group

  • Adding or removing it 

Enzymes speed up metabolic reactions by lowering energy barriers

• A catalyst

  • An agent that speeds up a reaction without being consumed or permanently changed

• Work efficiently and never be used up

  • If conditions allow it → varies with each enzyme

  • In body: body temperature (98 F), pH (6-8)

• An enzyme → catalytic protein

• Most end in ‘ase’

  • amylASE: helps change starches into sugars; found in saliva

  • maltASE: also found in saliva; breaks the sugar maltose into glucose; found in potatoes, pasta, and beer

  • helicASE: unravels DNA

Enzymes

• Catalytic protein: agents that speed up reactions without being consumed or permanently changed

  • Do this by lowering the required activation energy

• Very specific

  • Will only catalyze a single, specific reaction

  • Only binds to a specific reactant

  • Promotes bond-breaking and forming process

    • Lowering what takes to make the process started

• 4000 known biochemical reactions

  • Commercial uses include:

    • Synthesis of antibiotics

    • Detergents

    • Meat tenderizers

    • Brewing beer, making cheese, baking bread

  • Used outside body to help with everyday life

Activation barrier

• Every chemical reaction requires the making and breaking of bonds

• Activation barrier: energetic “hurdle” that a reaction must get over

  • What it takes for a reaction to occur

• Some reactions have higher hurdles and some have lower hurdles

  • Low activation barrier allows a reaction to happen quickly

• Enzymes lower energy barrier

Enzyme lifecycle

• 3D shape of the enzyme + the 3D shape of the substrate = specificity

  • Substrate (reactant) moves toward the enzyme’s active site

  • Chemical reaction is triggered by the enzyme

  • Enzyme releases the products

• BE FAMILIAR WITH LIFE CYCLE AND LABELING PARTS

Enzyme activity

• An enzyme’s activity can be affected by several factors:

  • Environment

    • Temperature: each enzyme has an optimal temperature

    • pH

  • Molecular components

    • Cofactors and regulatory molecules

  • Local conditions

    • Different tissues within the body

      • How much of enzymes should be produced

      • When enzymes should be produced

      • Where in cell enzymes should be produced

    • Different areas of the cell

    • Between different organisms

Enzyme activity: environment

• Temperature: each enzyme has an optimal temperature at which they function appropriately

  • Almost every human enzyme → 96 F

  • Optimal temperature for enzyme of thermophilic → 75 C; 200 F

• pH: each enzyme has an optimal pH at which they function appropriately

  • Humans → neutrality; around 7

    • Pepsin; stomach enzyme → very acidic

When things go “sub-optimal”: the denaturation of enzymes

• Extreme conditions break the bonds that hold the folded structure

• Denaturation: occurs when the structures of the proteins (enzymes) is disrupted due to unfolding

• Denaturation makes the enzyme inactive, and this process is irreversible

Enzyme regulation

• A cell’s metabolic pathways must be tightly regulated

  • To balance the catabolic and anabolic pathways and suit the cell’s current needs

  • For example: digestive cells in stomach work harder after a meal than when you are asleep

• Knows what you need when you need it very accurately

• Three primary ways to regulate enzymes:

  • When an enzyme should be active

  • Where an enzyme should be active

  • How much activity is needed

• Regulation can be positive or negative!

  • Turn on/off

  • Very important

  • Both equally important

Enzyme activity: molecular components

• Cofactors: non-protein enzyme components such as metals

  • Ex: NAD+ and NADP+

    • Coenzymes are organic cofactors including vitamins

• Regulatory molecules: extremely important!

  • Positive or negative regulation

    • Inhibition: negative

    • Activation: positive

    • Allosteric: negative or positive

• Concentration of these molecules is key

Enzyme inhibition

• Competitive inhibitors

  • Similar shape to the substrate

    • Competing for the active site

• Noncompetitive inhibitors

  • Bind to the enzyme at a different location

    • Changes the function → causes a slower reaction rate

  • Not in active site but changes the shape of the active site

• Inhibitors negatively affect an enzyme’s activity

  • Down regulates

  • Stops/slows down reaction

  • Negative correlation 

• Example: disulfiram is a competitive inhibitor of aldehyde oxidase

  • Causes build of acetaldehyde and nausea and vomiting

  • Used to treat alcoholism → stops the breakdown of alcohol

• Cyanide is a compound that acts as a noncompetitive inhibitor

  • Inner membrane protein in the mitochondria

Allosteric regulation: the “other object”

• Almost every situation with noncompetitive inhibitor, you can call it allosteric

  • Allosteric not necessarily noncompetitive

  • Have unique set of criteria 

• When protein function at one site is affected by the binding of a regulatory molecule at a separate site

  • Enzymes change shape when regulatory molecules bind to specific sites, affecting their function → can cause activation or inhibition

    • Make reaction go faster or completely stop it

• Nearly all cases of noncompetitive are allosteric regulation

  • However, allosterically regulated enzymes have set of unique properties that set them apart

  • I. e. Cooperativity, feedback inhibition

Allosteric regulation: cooperativity

• Protein function at one site affected by binding of a regulatory molecule at a separate site

  • Think polypeptides and proteins

• Inhibitor anywhere → whole protein gets shut down

Allosteric regulation: feedback inhibition

• Feedback inhibition

  • The end product of the metabolic pathway shuts down the pathway

    • Usually at an early step by inhibiting an upstream enzyme

• Important regulatory mechanism in cells

  • Example: ATP is an allosteric inhibitor for some enzymes involved in cellular respiration

Enzyme activity: local conditions

• Within the cell, enzymes may be

  • Grouped into complexes

  • Incorporated into membranes

  • Contained inside organelles

• Otherwise, found in different parts → different functionality

Energy transformations

• Sun is the source of energy for almost all organisms

• Solar energy is converted into a usable form that all organisms can use

  • Can indirectly use sunlight

• Energy also leaves the system as heat

• Energy in sunlight; energy out heat

  • Ecosystem

Respiration overview

• Living cells require transformations of energy from outside sources to perform their many tasks

• Cells extract energy from food

  • Generate ATP through the metabolic pathways involved that there is a close link between:

    • Transfer of energy 

    • Movement of electrons

      • Which have high energy levels

• Think of it as train station

  • Each process=train stop

  • Go from station to station until final destination

Cellular respiration (general)

• Most prevalent and efficient catabolic pathway

• Consumes oxygen and organic molecules like glucose

• Yields ATP (its purpose)

  • Regeneration of ATP keeps cell working

• Similar to combustion of vehicle

  • Engine; cell

    • Reaction: combustion; respiration

  • Transforming energy

    • Fuel: gasoline; eating food, oxygen

  • Power:

    • Move vehicle; work

  • Output:

    • Waste products: carbon dioxide and water

Redox reactions

• Oxidation-reduction reactions

  • Oxidation: loss of electrons during a reaction

  • Reduction: gain of electrons during a reaction

    • They take place simultaneously

    • OILRIG

      • Oxidation is loss, reduction is gain

• Reducing agent → oxidation reaction → oxidized

  • Reducing agent: glucose

  • Oxidized: carbon dioxide

• Oxidizing agent → reduction reaction → reduced

  • Oxidizing agent: oxygen

  • Reduced: water

• During cellular respiration (through series of enzymatic reactions)

  • Glucose is oxidized → produces carbon dioxide

  • Oxygen is reduced → produces water

• Other important coenzymes:

  • FAD+; FADH

  • NADP+; NADPH

Coenzymes

• non-protein molecules required for some enzymes to function

  • Act as electron carriers/shuttles

• Other important coenzymes:

  • FAD+; FADH

  • NADP+; NADPH

Examples of Redox Reactions

• Example: nicotinamide adenine dinucleotide (NAD)

  • Cofactor central to metabolism

  • Exists in two forms:

    • NAD+: oxidized form (fewest electrons)

      • Becomes reduced to form NADH

      • Accepts electrons during redox reactions

      • Least amount of negative charge → +

    • NADH: reduced form (most electrons)

      • Becomes oxidized to form NAD+

      • Donates electrons during redox reactions

      • Abundance of electrons 

Cellular respiration (specific)

• Energy-releasing chemical breakdown of fuel molecules

• Chemical energy of organic molecules is released to make ATP

• Provides energy for the cell to do work

• Prokaryotes do NOT have mitochondria

  • Still do respiration → don’t do it in the mitochondria

  • Aerobic respiration

• Energy needed for respiration is provided by the oxidation of glucose through a series of enzymatic reactions (steps)

  • To pass electrons to their carriers, usually NAD+ first

• Utilizes NAD+ and the electron transport chain

  • Goal is to produce ATP

• Not a single step → would be explosive

  • If one step, there would be explosions when you eat

  • A large release of energy (stored in bonds)... similar to the reaction of hydrogen and oxygen to form water

  • Want to slowly generate ATP

ATP in living systems

• ATP generation

  • By endergonic reactions

  • ADP undergoes phosphorylation

    • ADP + P → ATP

    • Releasing energy to do work

• Energy required can be obtained from

  • Substrate level phosphorylation (inefficient during cellular respiration)

    • Direct transfer for a phosphate group

    • Coupled exergonic/endergonic reactions during the breakdown of glucose

      • Chemical energy

    • Occurs during glycolysis and Krebs cycle (inefficient)

  • Oxidative phosphorylation (chemiosmosis and electron transport chain - VERY efficient)

    • Process that requires extra steps and ATP synthase

    • 90% ATP produced by this method (very efficient)

    • Occurs in the mt (mitochondria), cp (chloroplast), and membrane of aerobic prokaryotes

    • Uses energy from a proton gradient generated during ETC (electron transport chain)

Glycolysis

• Doesn’t occur in the mitochondria

Glycolysis: universal energy releasing pathway

• Greek: splitting of sugar

• First step in oxidation of glucose

• Occurs in the cell cytoplasm

  • Everything has cytoplasm rather than mitochondria

• Oxygen not required

• Inputs

  • 1 glucose

  • 2 NAD+

  • 2 ATP

• Products

  • 2 ATP (NET)

  • 2 NADH and 2 H+

  • 2 pyruvate

• Glucose goes in; pyruvate goes out

Glycolysis: energy investment

• First 5 steps → energy investment stage

  • Take glucose and use energy to transform the glucose

  • “Spending money”

    • Have to spend money to earn money

  • Use energy to convert glucose of pyruvate

• Kinase: enzymes that transfer phosphates (groups)

• Isomerase: enzymes that catalyze reactions involving structural rearrangements

  • Forms isomers

    • Same molecular formula but different arrangements

• Stage 1-2: use up 2 ATP

• Stage 3-4: use up another ATP molecule

• Why is energy invested?

  • Reaction becomes more ordered/organized

• Start with glucose (1 molecule) → series of changes → use up energy → more ordered system → G3P (know have 2 molecules)

  • G3P: transition molecule/intermediate molecule

    • Alert that we went from investment phase to payoff phase

Glycolysis: energy payoff

• Happens twice → each molecule of G3P

  • Undergoes last 5 stages of glycolysis

• Payoff phase yields:

  • 2 NADH → moved to ETC in mitochondria

  • 2 H+ (proton; hydrogen ion)

  • 4 ATP → can be used in cytoplasm for anabolic processes

  • 2 H2O

  • 2 Pyruvate → enters mitochondria, broken down in pyruvate oxidation and citric acid cycle

• One cycle of glycolysis makes 2 ATP

  • Only “net” 2 ATP

  • Eventually produces 4 but uses 2 ATP to make 4

    • Spend money to make money

Pyruvate oxidation

• Pyruvate is transported to the matrix of the mitochondria of eukaryotes

  • Prokaryotes do this in cytoplasm

  • Remember: 2 pyruvate per glucose

• Pyruvate cannot enter the citric acid cycle (CAC) unless it is altered

• Process produces carbon dioxide whenever a carbon is removed

• Titilizes coenzyme A (CoA)

  • Carrier compound that picks up, activates, and transports the transformed pyruvate

  • Results in acetyl CoA

    • Major function is to deliver the acetyl group to the next stage of glucose catabolism

• Input: 2 pyruvate

• Output: carbon dioxide, acetyl CoA

Citric Acid Cycle (Krebs Cycle)

• 8 enzymatic steps

  • Redox

  • Dehydration

  • Hydration

  • Decarboxylation 

• Occurs in the matrix of the mitochondria (double membrane through endosymbiosis)

  • Prokaryotes accomplish in their cytosol

• Does NOT directly consume oxygen

  • But DOES require it

• Produces very little ATP

  • Purpose is to gather electrons from the ETC

• Completes the energy-yielding oxidation of organic molecules

• Every turn of cycle: more electrons gathered

  • Because of oxidation of organic molecules

  • Harvesting electrons from enzymatic reactions

• Inputs: NO pyruvate; 2 acetyl CoA, 2 oxaloacetate, 3 NAD+, 1 FAD

• Outputs: 4 CO2, 3 NADH, 1 FADH, 2 ATP/GTP, H2O

Oxidative phosphorylation

• Occurs in the cristae (inner membrane)

  • Happens in cell membrane of prokaryotes

  • More surface area to perform electron transport chain

    • Efficient ATP production

• A LOT of ATP production (the most)

  • Bulk majority of energy

• Only pathway where O2 is an input

• Consists of:

  • Electron transport chain

    • Creates a H+ concentration gradient

    • Provides the energy to power chemiosmosis

  • Chemiosmosis

    • Generates ATP

    • Couples the process of electron transport to ATP synthesis

• Follow flow of electrons

Electron transport chain

• Electrons are passed from one component of the ETC to the next

  • Via a series of electron transporters embedded in the inner mitochondria membrane

  • Shuttle electrons from NADH and FADH2 to O2

• Electron flow is unidirectional → only go one way

• Oxygen is the final electron acceptor at the end of the ETC and creates water → reason why we breathe

  • Complex 4 get to oxygen → water

  • End of station/line for electron movement

  • Causing protons to be pumped out at each station

    • Gathering protons

    • Protons in matrix and membrane very different

• In the process…

  • Protons (H+) are pumped from the matrix to the intermembrane space

    • O2 is reduced to form H2O by gaining electrons from the ETC

  • Protons are returned to the matrix but must pass through ATP synthase which then is activated and adds a phosphate to ADP, making ATP again

Chemiosmosis

• Energy coupling mechanism

• Uses kinetic energy to form ATP from ADP+Pi

  • Through the energy generated from protons (H+) falling down its gradient (electrochemical gradient)

• ATP synthase

  • Integral protein (enzyme)

    • Bottom left gif

    • Phosphorylating as each proton passes through

  • Catalyzes the assembly of ATP

• H+ gradient

  • Stores energy

  • Referred to as a proton-motive force

  • Drives chemiosmosis in ATP synthase

Anaerobic Metabolism

• Absence of oxygen

Fermentation takes place in the absence of oxygen

• Fermentation → a type of anaerobic respiration

  • Catabolic process → partial degradation of sugars

  • Occurs in cytoplasm of ALL organisms

    • Both prokaryotes and eukaryotes

  • Enables some cells to produce small amounts of ATP

    • Without oxygen

    • Sometimes when organisms need it the most

• Consists of:

  • Glycolysis: universal pathway

  • NAD+ regeneration pathway

    • This varies based on the type of fermentation

    • 2 types:

      • Lactic acid fermentation

      • Alcohol fermentation

Lactic acid fermentation

• Occurs in many organisms

  • From bacteria to humans

• Pyruvate is converted to lactate

  • Directly regenerates NAD+

    • NADH is oxidized to NAD+

• No CO2 released here

• As featured in

  • Muscle cells

    • When O2 is limited

  • Mammalian red blood cells

    • No mitochondria

  • Some bacteria

    • Like the ones seen in yogurt

Pyruvate = final electron acceptor

Alcohol fermentation

• Occurs mainly in yeasts (esp. Anaerobic species)

• Pyruvate is converted to ethanol (EtOH)

  • 2 steps/reactions

    • Releases O2

    • Pyruvate → acetaldehyde → EtOH (alcohol)

• Releases carbon dioxide

  • Happens from transition of pyruvate to acetaldehyde

• Acetaldehyde is the final electron acceptor

Regulation

• Cells strive for efficiency

• This is why, if we eat more food (chemical energy) than we need, our bodies will convert it to a storage molecule (like fat or glycogen)

  • Excess amino acids result in the anabolic pathway in protein metabolism to be turned off/slowed down

  • Common mechanism: feedback inhibition

Heterotrophs

• “Other feeding” organisms

• Obtain their organic material from other organisms

• Are the consumers of the biosphere

• Anything above primary producer

Autotrophs

• “Self-feeding” organisms

• There are two types:

  • Photoautotrophs: use sunlight to make food

    • Plants, algae, and cyanobacteria

  • Chemoautotrophs: energy from inorganic compounds (chemicals) to make food

    • Thermophilic bacteria that live in a thermophilic environment

Locating photosynthesis

• Chloroplasts: major site of photosynthesis

  • Most abundant in leaves

    • Basically anywhere that is green

  • Highest density of chloroplasts in the mesophyll cells

• Chloroplast structure:

  • Double membrane: inner and outer

    • Same reason as mitochondria

    • Endosymbiotic origins

  • Stroma: inner space of the chloroplast

    • Contains the thylakoids/grana

    • Goo

    • Site of dark reactions

    • NOT STOMA → pores in leaves

  • Thylakoid: disk shaped structure containing chlorophyll

    • Site of light reactions

  • Grana: stacks of thylakoids

  • Lumen: inner space of the thylakoid

Tracking atoms through photosynthesis

• Just like cellular respiration:

  • Involves a series of complex metabolic pathways

    • Photochemical reactions

      • “Light reactions”

      • “Light dependent reactions”

      • Happens in presence of light

    • Biochemical reactions

      • “Dark reactions”

      • “Light independent reactions”

      • Calvin cycle

Photosynthetic reactants

• Before exploring the overall process of photosynthesis, let’s establish the sources of its components:

  • Water is absorbed by the roots of the soil

  • Carbon dioxide is acquired from the air as a result of gas exchange through the stomata

    • Singular = stoma

  • Sunlight (energy from sun) is absorbed in chlorophyll

The use of water in Photosynthesis

• Chloroplasts split water into hydrogen ions, oxygen, and electrons

  • Incorporates the electrons of hydrogen into sugar molecules

    • Requires a LOT of energy as an input and releases oxygen as a byproduct

      • Oxygen is a waste product

  • Redox reaction:

    • Water is oxidized, carbon dioxide is reduced

Light energy

• Form of electromagnetic energy (radiation)

  • Composed of photon particles that travel as waves

  • We can only see a fraction of this energy

    • Visible range of light energy (same range plants use)

• Represented on the electromagnetic spectrum

  • The entire range of electromagnetic energy

• Light reactions convert solar energy to chemical energy → ATP and NADPH

Wavelengths and the visible spectrum

• Wavelengths are typically measured in nm

  • Longer wavelengths

    • Crest farther apart

    • Carry less energy than short wavelengths

• Visible range (400-700 nm)

  • Violets have the shortest wavelengths

    • More energy

  • Reds have the longest wavelengths

    • Less energy

Light absorption

• Pigments: substances that absorb specific light wavelengths (photon energy)

  • Each has a unique absorption spectrum

  • Photosynthetic pigments: set of pigments that absorb visible light and transfer the energy form the photons

• Three main: 

  • Chlorophyll a

  • Chlorophyll b

  • B-carotene

Absorption spectrum

• Shows which wavelengths of light are being absorbed by a given pigment

  • Chloroplast pigments provide clues into which wavelengths are most effective for photosynthesis

• Peak at blue/violet and red; low at green

  • Absorb well/terribly

• Theodor engelmann: credited for demonstrating the action spectrum for photosynthesis

  • Measuring output of oxygen

  • Placed a filament of green algae in a light spectrum created by a prism

    • Exposed different segments of algae to different wavelengths

  • Put aerobic bacteria on the slide and observed where these grew best

    • Bacteria that requires oxygen to grow

    • Waited to see where bacteria would best grow → taking in oxygen and reproducing

    • Where there is oxygen → there is photosynthesis → where bacteria grows the most

  • Bacteria grew best in violet/blue and red sections

Comparing absorption vs action spectra

• Where they absorb most they act out/release oxygen the most

• Action spectrum resembles the absorption spectrum for chlorophyll a but does not match exactly

  • Close correlation

• Rate of photosynthesis → oxygen output

  • Peaks at wavelengths that absorb the most light (violet/blue and red)