BIOL 111 EXAM 2 :|

Fluid Mosaic Model

A mosaic of components (phospholipids, cholesterol, proteins, and carbohydrates) that give the membrane a fluid character.

Phospholipid Bilayer

polar heads face outward

hydrophobic tails face inward.

Integral Proteins

integrated completely into the bilayer

Integral membrane proteins (IMPs) have 1 or more hydrophobic regions (hydrophobic amino acids) and others that are hydrophilic.

Locations and number of regions determine how they arrange within bilayer.

Proteins

Function as transporters, receptors, enzymes, or in binding and adhesion

Attached to either phospholipid or integral protein

Can carry out similar functions to IMPs

Peripheral Proteins

occur only on the surfaces

Carbohydrates

3rd major component of PM

2-60 monosaccharides, branched or unbranched

Located on exterior surface of PM, bound to either proteins (forming glycoproteins) or to lipids (forming glycolipids).

Function in cell-cell recognition & attachment

Membrane Fluidity

Membrane needs to be flexible but maintain structure Fluidity is affected by:

• Phospholipid type –saturated FAs pack together more closely than unsaturated FAs

• fluidity greater with more unsaturated FAs

• Temperature – cold temperatures compress molecules making membranes more rigid

• Cholesterol - acts as a fluidity buffer

• keeps membranes fluid when cold but not too fluid when hot

Membranes Asymmetry

• inner surface differs from outer surface

• Interior proteins anchor fibers of cytoskeleton to membrane

• exterior proteins bind extracellular matrix

• glycoproteins bind to substances cell needs to import

Selectively Permeable

allows some molecules to pass but not others

• this allows cytosol solutions to differ from extracellular fluids

• Ex) all cells maintain an imbalance of Na+ and K+ ions between interior and exterior environments • Transport across a membrane can be either

• Passive – requires no energy

• Active – requires energy (ATP)

• Concentration gradient established

• substances accumulate along a range

Diffusion (Passive)

• occurs when a substance moves from area of high concentration down its concentration gradient

• In membranes this occurs through the lipid bilayer

• Net movement ceases once equilibrium achieved

• Only small nonpolar molecules (O2 , CO2 ) & lipid hormones can diffuse through membrane

Factors that Affect Diffusion Rates

• Concentration gradients - greater difference = faster diffusion

• Mass of the molecules - smaller molecules = faster diffusion

• Temperature – higher temperature = faster molecular movement

• Solvent density – dehydration = increased cytoplasm density = slower diffusion rates

• Solubility – more nonpolar (lipid-soluble) = faster diffusion

• Surface area – increased surface area = faster diffusion • Distance travelled –greater distance = slower rate

• important factor affecting upper limit of cell size

• Pressure – pressure forces solutions through membranes faster

• ex) kidney cell filtration rates affected by blood pressure

Facilitated Passive Transport

• Facilitated diffusion moves substances down their concentration gradients through integral transmembrane proteins

• Ions and small polar molecules

• 2 types of facilitated transport proteins:

1. Channel proteins

2. Carrier proteins

Channel Proteins

Top, bottom, and inner core are composed of hydrophilic AA – attract ions &/or polar molecules

• some open all the time

• Others are gated

• open when signaled Ex)

• Aquaporins - specific to H2O

• Muscle cells have gated ion channels allowing muscle contraction when opened

Carrier Protein

All carrier proteins are specific to a single substance

• bind to substance, change shape & “carry it” to the other side

• many allow movement in either direction

• concentration gradient-dependent

• ex) glucose transport proteins

Osmosis (Passive)

• diffusion of water across a membrane

• water always moves from an area of higher water concentration to one of lower water concentration.

• [water] inversely related to [solute]

• water moves from low [solute] to high [solute]

• differences in [water] occur when a solute cannot pass through a selectively permeable membrane

Tonicity

• how an extracellular solution can change the volume of a cell by affecting osmosis

• often correlated to osmolarity of a solution

• total solute concentration of a solution (permeable and non-permeable solutes)

When solutions with different osmolarities are separate by a membrane permeable to water but not the solute:

• water moves from the solution with lower osmolarity through the membrane

Hypotonic

extracellular fluid has lower osmolarity than the cytoplasm – water enters the cell

Isotonic

extracellular fluid has the same osmolarity as the cytoplasm – no net water movement (water still moves)

Hypertonic

extracellular fluid has higher osmolarity than the cytoplasm – water exits the cell

Osmoregulation

Organisms with cell walls (plants, fungi, bacteria some protists) prefer hypotonic solutions

• The pressure exerted by the PM against the CW (turgor pressure) is critical for cell function

• Hypertonic solution causes plasmolysis – PM detaches from the CW (wilting in plants)

Electrochemical Gradients

• arise from combined effects of concentration gradients and electrical gradients

• electrical gradients (cytoplasm contains more negatively charged molecules - neg ions & proteins – than the extracellular fluid) is critical for proper cell functioning

Active Transport

• Used anytime an ion or molecule (i.e. glucose) is transported through a membrane protein:

1. against its concentration gradient

2. against its electrochemical gradient

• Energy always required for active transport

• 2 types of active transport:

• Primary – ATP provides the energy

• Secondary – electrochemical gradient provides the energy

3 types of Protein Pumps

• Uniporter – carries 1 molecule or ion

• Symporter – carries 2 different molecules or ions in same direction

• Antiporter – carries 2 different molecules or ions in opposite directions

Primary Active Transport

moves an ion or molecule against its concentration gradient using ATP hydrolysis

Ex) Na+-K+ pump

• Moves 3 Na+ out and 2 K+ in

• uses 1 ATP

Secondary Active Transport

uses an electrochemical gradient created by primary active transport to move a different substance against its concentration gradient

Many amino acids and glucose enter the cell this way

Bulk Transport

import or export of molecules/particles too large to pass through a transport protein

• Energy is required

• Occurs through endocytosis or exocytosis

• endocytosis forms new intracellular vesicles from PM

3 types of endocytosis

In phagocytosis (cellular eating), the cell membrane surrounds a particle and engulfs it.

In pinocytosis (cellular drinking), the cell membrane invaginates, surrounds a small volume of fluid, and pinches together to form a vesicle.

In receptor-mediated endocytosis, uptake of a specific substance is targeted by binding to receptors on the external surface of the membrane.

Exocytosis

Vesicles containing substances fuse with the plasma membrane. The contents are then released to the exterior of the cell.

Bioenergetics

study of energy flow through a living system

Metabolism

all chemical reactions of a cell or organism

Metabolic pathway

series of biochemical reactions that converts one or more substrates into a final product

• Ex) sunlight energy captured during photosynthesis is used to synthesize glucose

• 6CO2 + 6H2O + energy → C6H12O6 + 6O2

• Ex) the energy stored in glucose is released during cellular respiration

• C6H12O6 + 6O2 → 6CO2 + 6H2O + energy

2 types of reactions/pathways

• Those that require energy and synthesize larger molecules are called anabolic.

• Those that release energy and break down large molecules into smaller molecules are called catabolic.

Chemical energy

– Energy stored in chemical bonds (potential) then released (kinetic)

ex: Gasoline stores potential energy in its bonds. When gasoline is burned it releases energy to move the car

Free Energy (Gibb’s Free Energy (G))

amount of energy available to do work (usable energy)

• All chemical reactions affect G

• ∆G = change in G after a reaction

ΔG = ΔH − TΔS

Where: ΔH is change in total energy of the system (enthalpy)

T is Temperature in Kelvins (°C + 273)

ΔS is change in entropy (energy lost to disorder)

Exergonic Reactions

If energy is released in a chemical reaction:

• ΔG < 0

• products will have less free energy than substrates

are spontaneous because they can occur without addition of energy

• Spontaneous reactions do not necessarily occur quickly

Endergonic Reactions

If a chemical reaction requires an input of energy:

• ΔG > 0

• products will have more free energy than substrates

Activation Energy

• the energy required for a reaction to proceed

• causes reactant(s) to become contorted and unstable, allowing bond(s) to be broken or made

• unstable state is called the transition state

• in transition state the reaction occurs very quickly

• Heat energy is the main source for activation energy in a cell

• Heat helps reactants reach transition state

• ex) rusting of iron over time

Thermodynamics

study of energy and energy transfer involving physical matter

Laws of Thermodynamics

• First Law of Thermodynamics – the total amount of energy in the universe is constant

• energy cannot be created or destroyed

• Second Law of Thermodynamics – the transfer of energy is not completely efficient

• in chemical reactions some energy is lost and unusable (i.e. heat energy)

• increases entropy (disorder)

ATP Structure

composed of adenosine backbone with 3 phosphate groups attached

• Adenosine = nitrogenous base adenine + 5-carbon ribose

• 3 phosphate groups = alpha, beta & gamma

• bonds between phosphate groups are high-energy

• when broken the products have lower free energy than reactants

ATP Hydrolysis

ATP + H2O → ADP + Pi + free energy

• ΔG = -7.3 kcal/mol (nearly double in cells)

• ATP is unstable and hydrolyzes quickly

• energy lost as heat if not coupled to endergonic reaction

• ⭐ when coupled with an endergonic reaction much of the energy can be transferred to drive that reaction

• is reversible

Sodium-Potassium Pump

Allows cells to maintain a low internal concentration of Na+and a high internal concentration of K+. This is an example of active transport. *Each pump performs these six steps 100 times per second (maximum speed).

3 Na+ for every 2 K+

Enzymes

• (primarily) protein catalysts that speed up reactions by lowering the required activation energy

• bind with reactants and promote bond -breaking and bond -forming processes

• very specific, catalyzing a single reaction

⭐do not change reaction’s Δ G

Enzyme-substrate Specificity

3D shapes (enzyme and substrates) determine specificity

substrates interact at enzyme’s active site

enzymes can catalyze a variety of reactions

Induced Fit

• at active site, a mild shift in shape optimizes reaction(s)

• slight changes maximize catalysis

⭐enzyme remains unchanged following reaction (resets)

How does an enzyme help the substrate reach its transition state?

• position two substrates so they align perfectly for the reaction

• provide an optimal environment (i.e. acidic or polar) within the active site for the reaction

• contort/stress the substrate so it is less stable and more likely to react

• temporarily react with the substrate (chemically change it) making the substrate less stable and more likely to react.

Enzyme regulation

• helps cells control environment to meet their specific needs

• ex) digestive cells in stomach work harder after a meal than during sleep

• enzymes can be regulated by:

• modifications to temperature and/or pH

• production of molecules that inhibit or promote enzyme function

• availability of coenzymes or cofactors

Competitive Inhibitors

have similar shape to substrate and compete w/ substrate for active site

Noncompetitive inhibitors

bind to enzyme at different location and slow reaction rate

Enzyme Regulation - Allostery

• Allosteric inhibitors modify active site = substrate binding is reduced or prevented

• Allosteric activators modify active site = affinity for substrate increases

Enzyme Cofactors

• Cofactors - inorganic ions (i.e. - Fe++, Mg++, Zn++ )

• DNA polymerase requires Zn++

Enzyme Coenzyme

• Coenzymes – organic molecules (i.e. -ATP, NADH + ) and vitamins

Feedback inhibition

end-product of pathway inhibits an upstream step

• important regulatory mechanism in cells

• ex) ATP allosterically inhibits some enzymes involved in cellular respiration

Redox Reactions

chemical reactions where electrons are transferred from one molecule to another

• Molecules that donate electron(s) are reducing agents and those that accept electron(s) are oxidizing agents

• Molecules that gain electron(s) after the reaction are reduced and those that lose electron(s) are oxidized

nicotinamide adenine dinucleotide (NAD)

occurs in an oxidized state (NAD+ ) or a reduced state (NADH).

• NADH carries 2e- and 1H+ more than NAD

• NAD+ accepts electrons from redox reactions; NADH donates them.

ATP in Living Systems

• hydrolysis of ATP → ADP + P i is exergonic

• provides energy for a coupled endergonic reaction

• phosphorylation - addition of a phosphate group to a molecule

• dephosphorylation - loss of a phosphate group

• Phosphorylated molecules tend to be less stable (more likely to react )

• ATP is generated when ADP is phosphorylated

• ADP + Pi → ATP (endergonic)

Substrate-Level Phosphorylation

a phosphate group that is covalently attached to another molecule is transferred to ADP to form ATP.

Oxidative Phosphorylation

a cellular process that harnesses the reduction of oxygen to generate high-energy phosphate bonds in the form of adenosine triphosphate (ATP).

• the only pathway where O2 is a reactant

• consists of an electron transport chain and chemiosmosis to generate ATP

• H+ concentration gradient provides energy to power ATP synthase

Glycolysis

• the 1st metabolic pathway of glucose metabolism

• includes 10 enzymatic reactions

• occurs in the cytoplasm

• O2 is not required (anaerobic)

• Reactants = 1 Glucose + 2 NAD+ + 2 ATP + 4 ADP

• Products = 2 Pyruvate + 2 NADH + 4 ATP + 2 ADP

Energy Investment Phase (Glycolysis)

The 1st half of glycolysis involves 5 enzymes and uses 2 ATP

• Glucose is phosphorylated 2x and then split into two 3- carbon molecules

• glyceraldehyde-3-phosphate (G3P)

Energy Payoff Phase (Glycolysis)

The 2nd half of glycolysis involves phosphorylation without ATP

• produces 2 NADH and 4 ATP molecules (2 net ATP)

• generates 2 pyruvate molecules

Oxidation of Pyruvate

• In eukaryotic cells, if oxygen is present, the 2 pyruvates enter mitochondria where each is converted to Acetyl CoA before entering the CAC:

• 1 CO2 is released (per pyruvate)

• It is oxidized, transferring e- to NADH

• coenzyme A is attached

Inputs: 2 pyruvate, 2 NAD+ 2 coenzyme A

Outputs: 2 CO2 , 2 NADH, 2 acetyl CoA

Citric Acid Cycle

• location: mitochondrial matrix

• Step 1 - the acetyl group from acetyl CoA is transferred to oxaloacetate to form citrate

• CoA transfers to –SH to replenish

• uses [ATP] as negative feedback mechanism

• through a series of reactions:

• citrate is oxidized (3 NADH & 1 FADH2 produced)

• 2 CO2 released

• 1 GTP or ATP produced

• final product of CAC is oxaloacetate

• cycle runs continuously in presence of sufficient reactants

Outputs per Glucose after Citric Acid Cycle

• 4 ATP (2 from glycolysis, 2 from CAC)

• 6 CO2 (2 from oxidation of pyruvate, 4 from CAC)

• 10 NADH (2 from glycolysis, 2 from oxidation of pyruvate, 6 from CAC)

• 2 FADH2 (from CAC)

• Glucose is completely oxidized at the end of CAC

• All possible electrons have been removed

Electron Transport Chain

• series of 4 electron transporters embedded in inner mitochondrial membrane (IM)

• shuttle electrons from NADH and FADH2 to O2

• protons (H+ ) are pumped from mitochondrial matrix to IM space

• O2 is reduced to form H2O

Complex I (ETC)

• NAD dehydrogenase protein enzyme w/ Fe-S cofactor

• FMN prosthetic group (from B-vitamin)

• receives e-s from NADH

• pumps 4 H+ from matrix into IM space

Complex II and Q (ETC)

• Complex II receives e-s from FADH2

• Q (ubiquinone) passes pairs of e-s from C I and C II to C III

Complex III (ETC)

• cytochromes B and C (cytochrome oxidoreductase)

• cyt C passes single e-s from C III to C IV

• pumps H+ into IM space

Complex IV (ETC)

• Fe and Cu cofactors hold oxygen until it is reduced by 2 e-s

• reduced oxygen picks up 2 Hs to make H2O

• pumps H+ into IM space

Chemiosmosis

• H+ needs a channel to move down gradient into matrix (potential energy)

• ATP synthase is H+ channel and enzyme for ADP + Pi ATP

• kinetic energy from H+ electrochemical gradient used to form ATP

ATP Yield from Cellular Respiration

• ~ 30-36 ATP per glucose generated varies by species:

• how many H+ pumped in ETC

• how efficiently NADH from glycolysis enters mitochondria

• NAD+ vs. FAD+ in different tissues

• Cellular respiration in total stores ~ 34% of the energy from glucose in ATP

• some intermediates (metabolites) used for other purposes

Metabolism Without Oxygen

• Glycolysis occurs in aerobic and anaerobic environments

• NAD+ must be constantly regenerated

• When O2 present:

• NAD+ created when NADH oxidized by ETC

• When O2 is lacking:

• organic molecule accepts e- (fermentation)

• fermentation regenerates NAD+

• There are 2 common types of fermentation

• Lactic acid fermentation

• Alcohol fermentation

• Some organisms use other final e- acceptor

• ex) methanogens and sulfur-reducing bacteria

Lactic Acid Fermentation

• muscle cells when O2 is limited

• mammalian RBCs

• some bacteria (i.e. those in yogurt)

• lactate dehydrogenase (LDH) catalyzes reaction

Alcohol Fermentation

• anaerobic yeast species

• 2 reactions

1. pyruvate + H+ → CO2 + acetaldehyde

• pyruvate decarboxylase

2. acetaldehyde + NADH + H+ → ethanol + NAD+

• alcohol dehydrogenase

Regulation of Cellular Respiration

regulated by many mechanisms:

• Hormonal control of glucose entry into cell

• Enzyme reversibility or irreversibility (able to exceed equilibrium)

• Enzyme sensitivity to pH changes due to lactic acid build-up

• Feedback controls

2 Types of Autotrophs

• Photoautotrophs – use sunlight to make food

• include plants (a), algae (b), and cyanobacteria (c)

• Chemoautotrophs – capture energy from inorganic compounds to make food

• thermophilic bacteria (e)

Heterotrophs

include animals, fungi, and most bacteria

• rely on sugars produced by autotrophs for energy

Photosynthetic Reactants

• H2O – absorbed by roots from the soil

• CO2 – acquired from air during gas exchange through stomata (small pores on leaf underside)

• O2 waste product exits through the stomata during exchange

• Sunlight

Photosynthesis Reaction Outcomes and Locations

• light-dependent reactions convert light energy to chemical energy

• makes ATP and NADPH (e- carrier)

• occur in thylakoid membranes of chloroplasts

• Calvin cycle uses the ATP and NADPH to make sugar (food)

• occurs in stroma of chloroplasts

Chloroplast Structure

• double membrane (outer & inner)

• stroma

• grana (stacks of thylakoids)

• lumen is inside thylakoid

Light Energy

• electromagnetic energy

• composed of photon particles that travel as waves

• Longer wavelengths carry less energy than shorter wavelengths

• We can see only a fraction of this energy (visible range)

• Plants use wavelengths in this range too

Pigments

absorb specific wavelengths of light

• each has a unique absorbance spectrum

• The main pigments of thylakoid membranes are:

• chlorophyll a

• chlorophyll b

• β-carotene (carotenoid)

Chlorophyll a and b

capture light for photosynthesis

• leaves are green (green wavelengths are reflected)

β-carotene

helps protect photosystems by dissipating excess energy

• also found in cells of carrots and oranges

Photosystems

• Photosystems II and I consists of a light-harvesting complex and a reaction center

• Pigments in the light-harvesting complex pass light energy to 2 special chlorophyll a molecules in the reaction center

• In the reaction center, the light excites an e- from the chlorophyll a pair, passing it to the 1st electron acceptor of the ETC

• a light-driven redox reaction

• The lost electron is then replaced

• In photosystem II the e- comes from the splitting of water, which releases oxygen as a waste product

• In photosystem I the e- comes from the ETC

Components of Thylakoid Membranes

• Photosystems II and I

• sites of light absorption

• an Electron Transport Chain (ETC)

• 2 enzyme complexes, NADP reductase and ATP synthase

Electron Transport Chain (Photosynthesis)

2 parts of the ETC in light reactions:

• first transports e- from PSII to PSI

• Plastoquinone (Pq)

• Cytochrome complex

• Plastocyanin (Pc)

• second transports e- from PSI to NADP reductase

• Ferredoxin

• final e- acceptor of the light reaction is NADP+ → yielding NADPH

like the ETC of cellular respiration:

• H+ gradient created as e- fall down chain

• pumped into the lumen space

• ATP synthase uses gradient to generate ATP (chemiosmosis)

Photosystem II

A protein complex found in the thylakoid membrane of chloroplasts. It plays a crucial role in the light-dependent reactions of photosynthesis by capturing light energy and using it to split water molecules, releasing oxygen and generating ATP and NADPH for the Calvin cycle.

Photosystem I

A key component of photosynthesis that absorbs light energy and converts it into chemical energy.

It is located in the thylakoid membrane of chloroplasts and plays a crucial role in the production of ATP and NADPH.

Photosystem I is involved in the second stage of photosynthesis, where it receives electrons from Photosystem II and uses them to generate energy-rich molecules.

3 Stages of the Calvin Cycle

1. Fixation: CO2 added to RuBP by enzyme RuBisCO to generate 2 x 3-PGA

2. Reduction: ATP and NADPH used to add e- and make sugar (G3P) 2x G3P → glucose

3. Regeneration of RuBP from G3P

Calvin Cycle

Part of photosynthesis where CO2 is converted into glucose. Takes place in the stroma of chloroplasts. Involves three phases: carbon fixation, reduction, and regeneration. ATP and NADPH from the light-dependent reactions are used. Key process for plants' energy production.

Photosynthesis and the Calvin Cycle

Step 1 of Glycolysis

Catalyzed by hexokinase, an enzyme with broad specificity that catalyzes the phosphorylation of six-carbon sugars.

Hexokinase phosphorylates glucose using ATP as the source of the phosphate, producing glucose-6-phosphate, a more reactive form of glucose.

This reaction prevents the phosphorylated glucose molecule from continuing to interact with the GLUT proteins, and it can no longer leave the cell because the negatively charged phosphate will not allow it to cross the hydrophobic interior of the plasma membrane.

Step 2 of Glycolysis

An isomerase converts glucose-6-phosphate into one of its isomers, fructose-6-phosphate (this isomer has a phosphate attached at the location of the sixth carbon of the ring).

An isomerase is an enzyme that catalyzes the conversion of a molecule into one of its isomers.

(This change from phosphoglucose to phosphofructose allows the eventual split of the sugar into two three-carbon molecules.)

Step 3 of Glycolysis

The phosphorylation of fructose-6-phosphate, catalyzed by the enzyme phosphofructokinase.

A second ATP molecule donates a high-energy phosphate to fructose-6-phosphate, producing fructose-1,6-bisphosphate.

In this pathway, phosphofructokinase is a rate-limiting enzyme.

It is active when the concentration of ADP is high; it is less active when ADP levels are low and the concentration of ATP is high.

Thus, if there is “sufficient” ATP in the system, the pathway slows down.

This is a type of end product inhibition, since ATP is the end product of glucose catabolism

Step 4 of Glycolysis

Employs an enzyme, aldolase, to cleave fructose-1,6-bisphosphate into two three-carbon isomers: dihydroxyacetone phosphate and glyceraldehyde-3-phosphate.

Step 5 of Glycolysis

An isomerase transforms the dihydroxyacetone-phosphate into its isomer, glyceraldehyde-3-phosphate.

Thus, the pathway will continue with two molecules of a glyceraldehyde-3-phosphate.

Step 6 of Glycolysis

Oxidizes the sugar (glyceraldehyde-3-phosphate), extracting high-energy electrons, which are picked up by the electron carrier NAD+ , producing NADH.

The sugar is then phosphorylated by the addition of a second phosphate group, producing 1,3-bisphosphoglycerate.

Step 7 of Glycolysis

Catalyzed by phosphoglycerate kinase (an enzyme named for the reverse reaction), 1,3-bisphosphoglycerate donates a high-energy phosphate to ADP, forming one molecule of ATP.

(This is an example of substrate-level phosphorylation.)

A carbonyl group on the 1,3-bisphosphoglycerate is oxidized to a carboxyl group, and 3-phosphoglycerate is formed.

Step 8 of Glycolysis

The remaining phosphate group in 3-phosphoglycerate moves from the third carbon to the second carbon, producing 2-phosphoglycerate (an isomer of 3-phosphoglycerate).

The enzyme catalyzing this step is a mutase (isomerase).