BIO 212 CUMULATIVE FINAL

What are the advantages of membranes in a cell?

They compartmentalize the cell.

How old is the universe?

~13.7 billion years

How old is the earth?

~4.6 billion years old

Miller/Urey experiments

Simulated conditions of early earth. Showed that organic molecules can be produced, further backing up the hypothesis that the beginning of life had an abiotic origin.

What are the likely characteristics of the earliest, simplest living forms?

1. Most likely unicellular2. Must have been self-replicating3. They had to acquire and/or convert energy4. They had to isolate themselves from the outside environment, (perhaps by a cell membrane).

When did life first appear on earth?

~3.6 billion years ago prokaryotic cells first appeared in the fossil record. The cells were cyanobacteria (blue-green bacteria) that formed stromatolites.

Stromatolites

Oldest known fossils formed from many layers of bacteria and sediment.

Emergence of eukaryotic cells

Thought to arise by endosymbiosis with prokaryotic cells because mitochondria and chloroplasts contain prokaryotic-like DNA.

Endosymbiosis

Occurs when one organism is consumed by another organism and lives inside the organism that consumed it

Radioisotope dating

can be done by measuring the ratio of isotopes in an object and back-calculating to how long ago it was formed

Cell theory

The theory that all living things are made of cells, that cells are the basic units of organisms, and that cells come only from existing cells" (Schleiden & Schwann, 1839)

Light microscope

An optical instrument with lenses that refract (bend) visible light to magnify images of specimens.

fluorescence microscope

powerful method that enables researchers to detect specific proteins, DNA sequences or other molecules that are made fluorescent by coupling them to a fluorescent dye (GFP or YFP)

electron microscope

a type of microscope that uses a beam of electrons to create an image of the specimen. It is capable of much higher magnifications and has a greater resolving power than a light microscope, allowing it to see much smaller objects in finer detail

prokaryotic cells

-lack a membrane-bound nucleus-much smaller than eukaryotic cells-bacteria is an example of a prokaryotic cell. bacteria contains: (1) a plasma membrane; (2) a single chromosome; (3) ribosomes, which synthesize proteins; (4) stiff cell wall; (5) few, if any, internal membrane-bound organelles.

eukaryotic cells

-can be unicellular or multicellular-defined as cells with "true" nuclei; wherein they possess a membrane-bound nucleus.-most have many membrane-bound organelles in the cytoplasm

the nucleus

-contains the cells DNA (nuclear genome)-surrounded by a double-membrane nuclear envelope-the nuclear envelope is studded with pores-RNA made in the nucleus needs to get out through the pores into the cytoplasm, while some proteins made in the cytoplasm need to get in through the pores into the nucleus

nuclear envelope

Double membrane perforated with pores that control the flow of materials in and out of the nucleus.

Chromatin

DNA in the nucleus is in the form of chromatin, (DNA + protein)

Animal cell

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Plant cell

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What structure do animal cells possess that plant cells do not?

1. golgi apparatus 2. centrioles

What structure do plant cells possess that animal cells do not?

1. cell wall2. chloroplast

cytoskeleton

Network of protein filaments within some cells that helps the cell maintain its shape and is involved in many forms of cell movement. Not static like scaffolding, rather the proteins can move and change to alter the cells shape and promote movement.

cytoskeletal elements

(In order from largest to smallest:) Microtubules, intermediate filaments, and actin filaments

Microtubules

A hollow rod of the protein tubulin in the cytoplasm of all eukaryote cells that make up cilia, flagella, spindle fibers, and other cytoskeletal structures of cells. Grow at PLUS ends, disassemble at MINUS ends.Assemble from the Microtubule Organizing Center (MTOC). In animal cells, this is called the centrisome.

Intermediate filaments

Cytoskeletal filaments with a diameter in between that of the microtubule and the microfilament. Intermediate filaments are composed of many different proteins and tend to play structural roles in cells.

Actin filaments

a thin type of protein filament composed of actin proteins that forms part of the cytoskeleton and supports the plasma membrane and plays a key role in cell strength, shape and movementformed by polymerization of actin molecules, bundled together in dense networks

Centrisome

composed of 2 centrioles, perpendicular to each other.

Centrioles

perpendicular

Kinesin

A large family of motor proteins that uses the energy of ATP hydrolysis to move toward the plus end of a microtubule. Can carry "cargo"- (different materials)- around the cell.

Railroad tracks

Microtubules act as railroad tracks for Kinesin.

Cilia and Flagella structure

Internal structure is an "axoneme" composed of interconnected microtubules. Axoneme has a complex "9+2" arrangement of microtubule doublets.Surrounded by the plasma membraneCritical motor elements are the dynein arms

Axoneme

Axoneme has a complex "9+2" arrangement of microtubule doublets.Surrounded by the plasma membraneCritical motor elements are the dynein arms

Dynein arms

protein extension from a microtubule doublet in a cillia or flagella that is involved in the energy conversion (ATP) that drives the bending of it, to create motion.ATP causes dynein to walk towards minus end (of microtubule) and pull towards plus end. Microtubule doublets are connected by spokes; creates a swimming motion

Motor protein in cilia and flagella

dynein arms

How does actin support movement?

By filament assembly/disassembly. Filament assemble at plus end. Elongates when filaments assemble at plus end faster than they disassemble at minus end.

Actin-Myosin interactions

Involved with muscle contraction.

What proteins are involved in muscle contraction?

Actin-Myosin interactions

Myosin

A motor protein. Converts the chemical energy in ATP into the kinetic energy of mechanical work. (Actin-myosin interactions)

Cytoplasmic streaming

the directed flow of cytosol AND organellesin plant cells, the movement occurs along actin filaments and is powered by myosin

cytosol

The soluble portion of the cytoplasm, which includes molecules and small particles, such as ribosomes, but not the organelles covered with membranes.

What is the importance of Actin-Myosin interactions in plant cells?

Cytoplasmic streaming; the directed flow of cytosol and organelles. The movement occurs along actin filaments and is powered by myosin

The motor protein that transports vesicles with cargo along microtubules is called...

Kinesin

John produces defective sperm with motionless flagella. His physician tells him that it may be a problem with the flagellar motor protein that drives the swimming motion of flagella. That motor protein is called...

Dynein

Protein secretion

A dynamic cellular process that delivers proteins outside the cell OR to different organelles within the cell.

Cellular secretory pathway

Proteins intended for secretion from the cell are synthesized on ribosome on the rough ER (RER).The RER is the entry to the secretory pathwayThe RER is a network of membrane-bound tubes and sacs studded with ribosomes.Proteins are then packaged into vesicles and trafficked through the pathway.

vesicles

small membrane sacs that specialize in moving products into, out of, and within a cell

George Palade

Discovered the secretory pathway. He studied protein secretion in pancreas cells.Conducted the Pulse-Chase experiment with pancreatic cells in culture to track proteins during the process of secretion. Newly synthesized proteins incorporated 3H-leucine during a "pulse" with to start the experiment.Then, the 3H-leucine was diluted out with unlabeled leucine during a "chase". Labeled proteins were followed during the chase by autoradiography in the electron microscope.

3H-leucine

a white, crystalline, water-soluble amino acid, C 6 H 13 NO 2, obtained by the decomposition of proteins and made synthetically: essential in the nutrition of humans and animals.

Pulse-Chase Experiment

Conducted with pancreatic cells in culture to track proteins during the process of secretion.Newly synthesized proteins incorporated 3H-leucine during a "pulse" to start the experiment.Then, the 3H-leucine was diluted out with unlabeled leucine during a "chase". Labeled proteins were followed during the chase by autoradiography in the electron microscope.

Pulse-Chase Experiment graphical representation

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How are proteins sorted out to different organelles (in the endomembrane system)?

the protein secretion pathway

endomembrane system

RER --> Golgi --> Lysosome OR outside of the cell

Lysosomes

Part of the endomembrane system.Contain digestive enzymes which digest materials brought into the cell.

What part of the cell is the "digestive system"?

lysosomes

if proteins are transported in membrane vesicles, then how do proteins get across the membrane barrier and inside the membrane vesicles?

The solution is to synthesize proteins by RIBOSOMES ON THE ENDOPLASMIC RETICULUM and insert the protein into the ER during synthesis.

The signal hypothesis

A protein destined for secretion has a GUIDE to direct it during synthesis to the ER. The guide is a short ER signal sequence on the front end of a protein. The ER signal sequence guides the growing protein and its ribosome to the ER.1.Binds to a signal recognition particle (SRP) that then guides the ribosome to a receptor on the ER.2. Protein is cotranslationally inserted through a translocon into the ER. It is inserted into the ER as it is being synthesized.

Moving from ER to Golgi

Proteins are then transported into vesicles that:1. bud off from the ER with their protein cargo inside2. Fuse with the membrane on the "cis face" of the Golgi apparatus3. Exit the "trans face" in vesiclesEach protein exiting the Golgi apparatus has a ticket for vesicle transport to a particular cellular location.Each type of transport vesicle also has a tag that targets the vesicle to the correct destination.

Sorting proteins

Vesicle-transported proteins are targeted to different organelles.1. Proteins are tagged2. Proteins are sorted 3. Vesicles bud4. Proteins interact with receptors5. Delivery

Which organelles are not in the endomembrane system? Why?

Mitochondria and chloroplasts. Their proteins are synthesized on free ribosomes in the cytosol and actively imported after synthesis.They also contain special organelle targeting sequences. Organelle receptors recognize the targeting sequences and import the proteins.

Membrane bilayer structure

Bilayer structure is largely conferred by phospholipids, a major component of cell membranes. HydrophilicHydrophobicHydrophilic

phospholipids

-are amphipathic, meaning that the individual molecules have both hydrophilic and hydrophobic properties-membrane phospholipids self organize into structures that are compatible with their amphipathic character.

phospholipid self organization

-self organize with their HYDROPHILIC ends facing the aqueous environment and their HYDROPHOBIC tails creating their own HYDROPHOBIC environment

lipid micelles

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lipid bilayers

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How is the lipid bilayer held together?

held together by HYDROPHOBIC forces which maintain phospholipids in a HYDROPHOBIC environment

Fluid mosaic model

Membrane is semifluid because the phospholipids are NOT COVALENTLY bonded together. The lipids and proteins float about within the plane of the membrane.

phospholipid movement

membranes need to be semifluid in order to function.

Membrane proteins

Cell membranes also contain proteins as well as phospholipids.Membrane proteins have transmembrane domains inserted in the membrane (like a screw). These domains are alpha-helical and contain hydrophobic amino acids.

Fluid mosaic model of membrane structure

Cell membranes are considered to be a mosaic of proteins and other constituents embedded in a sea of phospholipids

Freeze fracture

Freeze fracture electron microscopy provides views inside the membrane.It splits the lipid bilayer in two.It tends to split the membrane bilayer apart because the monolayers are not bonded together. Allows you to see the proteins embedded in the membrane.

protein bleaching

FRAP using GFP. The GFP tagged proteins float freely in the membrane, and the spot will fade with time as unbleached molecules around it diffuse into the bleached spot.

Why do phospholipids tend to form micelles or membrane bilayers? Because these structures...

A.) Are compatible with the amphipathic properties of phospholipidsB.) Allow for the hydrophilic heads of phospholipids to face an aqueous environmentC.) Allow for the fatty acid tails of phospholipids to create a hydrophobic environmentD.) All of the above.

Phospholipids can diffuse freely within the plane of the membrane because...

A.)They are not bonded togetherB.) They are amphipathicC.) They have hydrophilic head groupsD.) They have hydrophobic tails

Fatty acid saturation

Fatty acid chains on phospholipid tails can be saturated (all carbons with H2) or unsaturated (some carbons without H2, but with double bonds)Unsaturated fatty acids with shorter, kinked tails disrupt the ordered bilayer and produce greater membrane fluidity.

Membrane permeability

Cell membranes are semipermeable.Permeability of a membrane is its tendency to allow substances to pass across the membrane.Phospholipid bilayers have selective permeability...-SMALL or NONPOLAR molecules move across phospholipids bilayers rapidly-CHARGED or LARGE POLAR substances cross slowly, if at all.

Measuring membrane permeability

Using Artificial-membrane experiments....How rapidly can different solutes cross the membrane?What properties of a solute affect its permeability?

Solutes, Solvents, and Solutions

Solutes are substances dissolved in a solvent. Altogether they make a solution.

Membrane permeability scale

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For a fish to survive in the bottom of an Iowa pond over the winter, the fish needs...

A.) Longer fatty acids in its membrane phospholipidsB.) More saturated fatty acids in its membrane phospholipidsC.) More unsaturated fatty acids in its membrane phospholipidsD.) All of the above

Unsaturated fatty acids

Disordered. Greater fluidity. Like oil.

Saturated fatty acids

Rigid, ordered. Less fluidity. Like butter.

Order these substances by their membrane permeability (greatest to least)

Water, Glucose, Sodium

Animal cell membranes contain cholesterol

General structure of a steroid, such as cholesterol.Cholesterol is highly nonpolar (hydrophobic).

Cholesterol

Is a steroid.Is highly nonpolar.Therefore, is hydrophobic.Is readily incorportated into cell membranes.

Does cholesterol affect membrane permeability?

Glycerol permeability increases with temperature. Membrane fluidity increases with temperature as does membrane permeability.Cholesterol reduces membrane permeability.

Does cholesterol affect membrane permeability?

Cholesterol reduces the fluidity of the membrane by constraining the movement of the fatty acid tails.

Movement of solutes and solvents

Solute and solvent molecules:-Have thermal energy-Are in constant, random motion called diffusion

Diffusion

Movement of molecules from an area of higher concentration to an area of lower concentration.

Passive Transport

Diffusion process that does not require any extra input of energy

Active Transport

Diffusion process that requires extra energy to move substances across the membrane

Concentration gradient

The NET MOVEMENT of solutes and solvents across a membrane by PASSIVE TRANSPORT follows concentration gradients.A concentration gradient is created by a DIFFERENCE in solute or solvent concentrations across a membrane.Molecules and ions diffuse RANDOMLY DOWN a concentration gradient:-From high concentration to low concentration-Increases ENTROPY-Is SPONTANEOUS

Equilibrium

Occurs when the molecules or ions are EQUALLY DISTRIBUTED across membranes.Molecules are STILL MOVING randomly, but there is NO NET movement.

osmosis

the movement of water is a special case of diffusion called osmosis.Water moves from regions of LOW SOLUTE concentration to regions of HIGH SOLUTE concentration.OR looking at it another way, water moves from regions of HIGH SOLVENT to LOW SOLVENT.

Tonicity

describes the RELATIVE CONCENTRATION of suspending solutions outside of a cell that determines the DIRECTION AND EXTENT of diffusion across a membrane.

Hypertonic solution

the solution outside the cell has a HIGHER solute concentration than inside.Net movement of water OUT of the cell, the cell SHRINKS.

Isotonic solution

The solution outside the cell has about the SAME solute concentration as inside.Water will continue to flow in both directions, but there will NOT be a net movement of water.

Hypotonic solution

The solution outside the cell has a LOWER solute concentration than inside. Net movement of water INTO the cell. Vesicle SWELLS or even BURSTS.

Permeability of solutes

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Facilitated diffusion

Some solutes, such as larger molecules or ions (glucose, sucrose, Cl-, K+, Na+) cannot cross membranes because they are MEMBRANE IMPERMEABLE. However, a specific carrier may facilitate their movement across a membrane.Such molecules move PASSIVELY (no extra energy) by FACILITATED DIFFUSION from a region of HIGH SOLUTE concentration to LOW SOLUTE concentration.

Facilitated diffusion- glucose transport

Glucose can be moved by facilitated diffusion via a carrier or transporter.Lipid bilayers are only moderately permeable to glucose, yet glucose is a CRITICAL NUTRIENT and cells often need plenty of it. A glucose carrier named GLUT-1 increases membrane permeability to glucose. Glucose is transported across the membrane DOWN A CONCENTRATION GRADIENT by the glucose carrier, GLUT-1.GLUT-1 undergoes a CONFORMATION CHANGE to transport glucose across the membrane.

Ion channels

Ion channels are specialized membrane proteins that allow for the movement across membranes of SMALL, UNCHARGED COMPOUNDS.Unlike carriers and facilitated diffusion, ion channels DO NOT UNDERGO A CONFORMATIONAL CHANGE to allow passage of an ion.However, like facilitated diffusion, ions diffuse PASSIVELY (no extra energy) through channels down their ELECTROCHEMICAL GRADIENT.Ions channels can be SELECTIVE allowing only the passage of certain ions. They can also be GATED and will OPEN AND CLOSE in response to various SIGNALS.An example or an ion channel is Cystic fibrosis transmembrane conductance regulator (CFTR).

Cystic fibrosis transmembrane conductance regulator (CFTR)

Example of an ion channel.Mutations in the CFTR gene result in Cystic Fibrosis. CF presently affects about 30,000 children and adults in the US.CFTR mutations lead to dysregulation of EPITHELIAL FLUID TRANSPORT and the production of STICKY MUCUS that can BLOCK AIRWAYS.

Experiment: Is CFTR a chloride ion channel?

1. Create a PLANAR BILAYER in which CFTR is embedded2. Create a CHLORIDE GRADIENT across the membrane3. Record an ELECTRICAL CURRENT across the membraneThe current record demonstrates that CFTR supports ION FLOW and that ATP OPENS the channel.

Active transport

Cells can transport molecules or ions by ACTIVE TRANSPORT.-AGAINST a chemical or electrochemical gradient-The transport REQUIRES ENEGY, such as ATP.PUMPS are MEMBRANE PROTEINS that actively transport molecules across the membrane.-They move uncharged molecules or ions AGAINST their concentration gradients.

Facilitated diffusion VS. Active transport

Both require a TRANSPORTER, however one moves solutes WITH A GRADIENT, the other AGAINST.

Electrochemical gradients

Gradients can be ELECTRICAL (based on charge, membrane potential), CHEMICAL, or BOTH. Na+ show a strong tendency to move inside the cell based on the electrochemical gradient. However, cells have to maintain a LOW INTERNAL concentration of Na+ for PROTEIN SYNTHESIS.To do this, they use a sodium-potassium pump which uses ATP to move Na+ AGAINST its electrochemical gradient.

Pumps (Na+/K+ pump)

The cell also needs to maintain a POSITIVE CHARGE to OUTSIDE of the membrane. The pump needs to pump Na+ OUT OF THE CELL to maintain a POSITIVE CHARGE to the outside. However, the Na+/K+ pump obligatorily EXCHANGES Na+ for K+, another positive charged ion, each pumping cycle. In that case, the Na+/K+ pump need to PUMP OUT MORE Na+ than it BRINGS IN K+....SO.. With each cycle, the pump PUMPS OUT 3 Na+ and BRINGS IN 2 K+.

Sodium-Potassium Pump

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Energy in Chemical Reactions

There are two types of energy:Kinetic energy: Energy of motion. At a molecular level, kinetic energy is THERMAL energy.Potential Energy: Stored energy, energy of position or configuration. At a molecular level, most potential energy is CHEMICAL energy.

First Law of Thermodynamics

Energy cannot be created or destroyed, but can be CONVERTED to various forms. Organisms capture, convert, utilize, and store energy.

Photosynthesis

Most energy in biological systems comes from the sun and is capture in plants by photosynthesis.Plants convert solar energy into chemical energy and store the energy in biological molecules (starch, sugar, etc.)

Chemical reactions that release energy

The oxidation of glucose is a chemical reaction that RELEASES ENERGY.Chemical reactions that release energy are called EXERGONIC reactions.They release energy because the products have LESS free energy than the reactants.

Exergonic reactions

RELEASE energy because the products have LESS free energy than the reactants.OCCUR SPONTANEOUSLY (without the input of energy)

Gibbs Free Energy Change (𝚫G)

The gain or release of energy in a chemical reaction can be expressed as CHANGE IN FREE ENERGY (𝚫G)𝚫G= 𝚫H-T𝚫S[Gibbs free energy change= Change in Enthalpy (chemical energy) - Temperature (degrees Kelvin) of change in Entropy (disorder.]𝚫G= Gibbs free energy change𝚫H= Change in ENTHALPY (chemical energy)𝚫S= Change in ENTROPY (disorder)T= temperature in degrees Kelvin

...chemical reactions that release energy

The change in free energy (𝚫G) is given in kcal/mol.-Kilocalorie = 1000 calories-1 calorie = the amount of heat needed to raise 1 gram of water 1 degree C.-1 kilocalorie = 1 calorie (common Calorie, capital C)The free energy change (𝚫G) for the oxidation of glucose is -686 kcal/mol.𝚫G is a NEGATIVE NUMBER because the PRODUCTS of the reaction have LESS FREE ENERGY than the reactants. Only EXERGONIC REACTIONS with negative 𝚫G's will occur SPONTANEOUSLY (without the input of energy)

Calories and kilocalories

-Kilocalorie = 1000 calories-1 calorie = the amount of heat needed to raise 1 gram of water 1 degree C.-1 kilocalorie = 1 calorie (common Calorie, capital C)

Chemical reactions that require energy

6CO2 + 6H2O + energy--> C6H12O6 + 6O2The reverse reaction, the synthesis of glucose, which occurs during PHOTOSYNTHESIS in plants, is an energy REQUIRING reaction.Reactions that require the input of energy are called ENDERGONIC reactions.They require energy because the products of the reaction have MORE FREE ENERGY than the reactants.

Synthesis of glucose

Example of an ENDERGONIC reaction that REQUIRES an extra input of energy. The free energy change (𝚫G) for the synthesis of glucose is +686 kcal/mol.𝚫G is a POSITIVE number because the PRODUCTS of the reaction have MORE FREE ENERGY than the reactants.Endergonic reactions with positive 𝚫G's do NOT OCCUR SPONTANEOUSLY (because they require the input of energy).

Endergonic reactions

REQUIRE INPUT of energy because the products of the reaction have MORE FREE ENERGY than the reactants.DO NOT OCCUR SPONTANEOUSLY (because they require the input of energy)

Exergonic vs. Endergonic reactions

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Examples of exergonic reactions

Hydrolysis reactions RELEASE energy: ATP + H2O --> ADP +iP + energy. (𝚫G= -7.3 kcal/mol)Oxidation/reduction reactions RELEASE energy (example glucose oxidation: 𝚫G= -686 kcal/mol)

Oxidation/reduction reactions (redox reactions)

Exergonic. Do not require any extra energy. Products have less free energy than the reactants. Negative 𝚫G.Oxidation/reduction reactions involve the TRANSFER OF ELECTRONS....Oxidation involves the LOSS of electrons (Reactant A --> Product A + e-)Reduction involves the GAIN of electrons (Reactant B + e- --> Product B)However, Redox reactions are always BALANCED. For every oxidation (electron loss), there is a reduction (electron gain).

Electrons accompanied by Protons

Each electron transferred from one molecule to another during a Redox reaction is usually accompanied by a proton (H+)A molecule that is oxidized LOSES a proton (-H+) and has LOWER POTENTIAL ENERGY.A molecule that is reduced GAINS a proton (+H+) and has HIGHER POTENTIAL ENERGY.

Nictotinamide adenine dinucleotide (NAD+)

Is a major ELECTRON carrier in redox reactions.It is reduced to form NADH (because reductions GAIN a H+)

NADH

Reduced form of NAD+. NADH is the ENERGETIC form, readily DONATES ELECTRONS to other molecules, and had REDUCING power.

ATP (Adenosine triphosphate)

Is the most common ENERGY carrier.Provides FUEL for most cellular activitiesHas HIGH potential energyIts formation stores energy, while its hydrolysis of its phosphate groups releases energy.Allows cells to do work.

Energy from ATP

Hydrolysis of the bond between the two outermost phosphate groups results in:-ADP and Pi (inorganic phosphate, H2PO4-)-Reaction is EXERGONIC (𝚫G= -7.3 kcal/mol)

Hydrolysis

Breaking down complex molecules by the chemical addition of water

Energetic coupling

Energetic coupling can occur between EXERGONIC and ENDERGONIC reactions.Allows chemical energy RELEASED from one reaction to DRIVE another reactionReactions must be PHYSICALLY COUPLED, i.e., they must occur on the same enzyme(Like 2 gears turning in opposite directions)

Reaction kinetics and enzymes

Enzymes are PROTEIN CATALYSTS that accelerate chemical reactions.-Most biological chemical reactions only occur at MEANINGFUL RATES in the presence of an enzyme. They may accelerate a chemical reaction a MILLION FOLD!Enzymes are very SPECIFIC for the reaction they catalyze.-Bring reactants (SUBSTRATES) TOGETHER to facilitate reactions-SUBSTRATES bind to an enzyme's ACTIVE SITE to form a SUBSTRATE/ENZYME COMPLEX.

Transition state

The formation of a SUBSTRATE/ENZYME COMPLEX promotes the INTERACTION OF SUBSTRATES and allows for the development of TRANSITION STATE for the reaction.

The transition state facilitates the reaction

1. INITIATION: Reactants bind to the active site in a specific orientation, forming an enzyme/substrate complex.2. TRANSITION STATE FACILITATION: Interactions between enzyme and substrate lower the activation energy required.3. TERMINATION: Products have lower affinity for active site and are released. Enzyme is unchanged after the reaction.

The transition state lowers the activation energy

The ACTIVATION ENERGY (Ea) is the amount of free energy required to reach the TRANSITION STATE. Enzymes STABILIZE the transition state, LOWER the ACTIVATION ENERGY for the reaction, but DO NOT CHANGE the 𝚫G for the reaction.

Reaction kinetics

What determines the rate (kinetics) of a reaction?-We have considered the change in FREE ENERGY in a reaction, but free energy changes do NOT determine the RATE of a reaction, only whether the reaction can occur SPONTANEOUSLY.Changes in free energy are THERMODYNAMIC PROPERTIES of a reaction, NOT KINETIC PROPERTIES.Rates of reactions depend on TEMPERATURE, however, we tend to discount differences in temperature because in most organisms reactions occur at physiological temperatures.

Substrate (Reactant) concentrations

Rates of enzyme-catalyzed reactions are also affected by substrate concentrations.The rate of enzyme-catalyzed reactions:-INCREASE LINEARLY at LOW SUBSTRATE concentrations as more substrate/enzyme complexes are formed-SLOW as higher substrate concentrations as substrate binding sites become more FULLY OCCUPIED.Reached MAXIMUM RATE (Vmax) at high substrate concentrations when substrate binding sites are FULL OCCUPIED.Thus, enzyme-catalyzed reactions are SATURABLE.Uncatalyzed reactions do not show saturation kinetics.

Enzyme kinetics

The velocity (rate) of an enzyme reaction increases with increasing substrate concentration.Maximum velocity (Vmax) is achieved at INFINITE substrate concentration when all substrate binding sites are occupied.The BINDING AFFINITY of the substrate for the enzyme is the substrate concentration at HALF MAXIMAL VELOCITY (Vmax/2)The SUBSTRATE BINDING AFFINITY is expressed as Km (Michaelis constant), which is given as a molar concentration.

Michaelis constant

Km: Substrate concentration at which the reaction velocity is half its maximum, unique for each enzyme-substrate pair and gives information about affinity of enzyme for its substrate (lower means not much needed to get reaction to half maximum rate, equals high affinity).

binding affinity

the tightness, or strength of binding to a receptor in the communication process

Competitive inhibition

Occurs when a molecule similar to the substrate competes with the substrate for access to the active siteCompetitive inhibitor can be a REGULATORY MOLECULE or a DRUG.Effectively dilutes the concentration of the substrate and raises the Km for the reaction

Statins

The most widely used drugs in America. Inhibit HMG reductase, an enzyme on the pathway for CHOLESTEROL biosynthesis.

Allosteric (non competitive) inhibition

Occurs when a molecule causes a CHANGE IN ENZYME SHAPE by binding to the enzyme at a location OTHER THAN THE ACTIVE SITE.Allosteric inhibition can DEACTIVATE an enzyme.

Metabolic pathways

Enzymes work together in METABOLIC PATHWAYS.-A series of reactions-Each catalyzed by a different enzyme-Enzymes guide reactions in a metabolic pathway by ACCELERATING THE RATES OF REACTIONS.Enzymes are HIGHLY SPECIFIC for their substrates and the reactions they catalyze. As a result, they bring order to the COMPLEX WEB OF METABOLIC REACTIONS.

Enzyme regulation

Activities of enzymes can be altered by PROTEIN MODIFICATION.The most common modification is PROTEIN PHOSPHORYLATION, which changes the structure and activity of an enzyme.

Feedback inhibition

Occurs when a metabolic pathway is INHIBITED by the PRODUCT of that pathway.Pathway shuts down when there is an OVERSUPPLY of a product.

Your body's cells use and synthesize ~10 MILLION ATP molecules PER SECOND

Cellular enzymes can catalyze more than 25,000 REACTIONS PER SECOND

cellular respiration

Process by which the chemical energy stored in "food" is released and captured in the form of ATP.ATP can then be used to do "work."Carbohydrates, fats, and proteins can all be used as food sources in cellular respirationBUT the utilization of glucose is the most common example of the reactions and pathways involved.

Glucose and cellular respiration

Glucose is utilized through a long series of reactions to form carbon dioxide and water. The overall reaction for cellular respiration is shown in the picture. The ΔG = -686 kcal/mol, meaning that the cellular respiration of glucose is an exergonic reaction.The released energy (change in free energy) is used to synthesize ATP from ADP and Pi. In other words:ADP + Pi --> ATPΔG = +7.3 kcal/mol, meaning that the synthesis of ATP is an endergonic reaction.

About how efficient is cellular respiration in making ATP, given that the number of ATPs made per glucose by cellular respiration is 29?

~30%

Mitochondria

Much of cellular respiration occurs in the mitochondria.Cristae are sacs of inner membrane joined to the rest of the inner membrane by short tubes.

Steps in cellular respiration

1. Glycolysis, occurs in the cytosol. Glucose is broken down to pyruvate.2. Pyruvate processing (oxidation), occurs in the mitochondria. Pyruvate enters the mitochondrion and is converted to acetyl CoA.3. Citric acid (TCA) cycle, occurs in the mitochondria. Acetyl CoA and its derivatives are oxidized to CO2.4. Electron transport and oxidative phosphorylation, occur in the mitochondria. Oxidation reactions lead to ATP production.

Glycolysis

Glycolysis consists of:- An energy investment phase- Followed by an energy payoff phase.ATP is synthesized through substrate level phosphorylation. Differs from oxidative phosphorylation in later steps.

Phosphorylation

The transfer of a phosphate group, usually from ATP, to a molecule. Nearly all cellular work depends on ATP energizing other molecules by phosphorylation.

oxidative phosphorylation

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substrate level phosphorylation

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Net energy production by Glycolysis

2 NADH + (4 ATP - 2 ATP) = 2 NADH + 2 ATP

Energy production in Glycolysis

When there is enough energy (ATP) around, the cell slows glycolysis.High levels of ATP block this step in glycolysis.This step is catalyzed by an enzyme called phosphofructokinase and its activity is blocked by feedback inhibition.

Pyruvate uptake and processing (oxidation)

During these reactions in the mitochondria:- Pyruvate is taken up- Another NADH is synthesized- One of the carbon atoms in pyruvate is oxidized to CO2- Acetyl CoA is made

Net Energy production by Pyruvate processing

Net energy production by Pyruvate Processing (mol/mol glucose)2 NADH

The citric acid (TCA) cycle

Each cycle produces high energy compounds:3 NADHs1 GTP1 FADH2(note: one glucose can drive two cycles)

Net energy production by the TCA cycle

6 NADH + 2 GTP + 2 FADH2(note: a mol of NADH can usually drive the production of 3 ATPs)

Order these processes by the amount of energy they generate (highest to lowest).

Citric acid cycle, glycolysis, pyruvate processing

Why is the citric acid cycle considered to be a cycle? Because it...

Regenerates oxaloacetate

How is ATP made from NADH and FADH2?

NADH and FADH2 from the TCA cycle donate high energy electrons to the electron transport chain.- The electrons are transported from one electron carrier to another as electrons move down the electron transport chain.- Energy is released at each step of the chain as electrons lose reducing potential.O2 is the final electron acceptor-This is why O2 is required for cellular respiration!

Electron transport

During electron transport in mitochondria, electrons are transported down the electron transport chain, releasing energy at each step.

Electron transport chain

The electron carriers are:-Four large multiprotein complexes and cofactors in the mitochondrial inner membrane called complexes I-IVUbiquinone (Q) and cytochrome c are mobile carriers- Transfer electrons between complexes

The Chemiosmotic Hypothesis

How is the energy released from electron transport captured to drive ATP synthesis?Peter Mitchell proposed that the energy was captured by the production of proton gradient.This radical idea was known as the Chemiosmotic Hypothesis.

Proton pumping

As electrons are transported, protons are pumped into the intermembrane space from the mitochondria matrix.- By complexes I and IV and by Q

Proton motive force (PMF)

The pumping of electrons creates a gradient of protons across the inner mitochondrial membrane.- The proton gradient is an energy store referred to as a proton motive force (PMF).

Proton gradient

youtube video (??)

ATP synthase structure

The PMF drives a turbine called an ATP synthase in the mitochondrial inner membrane.Makes ATP as it rotatesConformation changes in the rotor drives ATP synthesis

ATP synthase

The ATP synthase is an enzyme complex consisting of two components:1. An ATPse "knob" (F1 unit)2. A membrane-bound, proton-transporting base (F0 unit).

Testing the Chemiosmotic Hypothesis

The Chemiosmotic Hypothesis was tested to determine whether the PMF, but not electron transport, drives ATP synthesis.This was done by determining whether bacteriorhodopsin could drive ATP synthesis in vesicles with artificial membranes.In response to light, bacteriorhodopsin transports protons across a membrane creating a PMF.RESULTS: The findings supported the chemiosmotic hypothesis, and demonstrated that only the PMF and not electron transport was required to ATP synthesis.

chemiosmotic hypothesis

look up better diagrams online lol

What would happen in the previous experiment, if an ionophore, a membrane permeable proton carrier, had been added to the membranes?

ATP would not be made.

What is the difference between the way that ATP is made during glycolysis compared to oxidative phosphorylation? The ATP made during glycolysis...

Occurs by substrate-level phosphorylation

Coupling e- transport to ATP synthesis

Electron transport is tightly coupled to ATP synthesis even though the coupling is indirect, through a proton gradient.- If ATP synthesis is blocked, the hydrogen ion concentration (PMF) builds up, preventing further electron transport.-If electron transport is blocked, the PMF breaks down,* and ATP synthesis shuts down.

Oxidative phosphorylation: recap

The energy released as electrons are transported down the electron transport chain.- Is used to pump hydrogen ions (protons) across the mitochondrial inner membrane into the intermembrane space.- Forms a gradient of hydrogen ions (PMF) across the mitochondrial inner membrane.PMF drives ATP synthesis by the ATP synthase. This mode of ATP production:- couples phosphorylation of ADP (to form ATP) to NADH and FADH2 oxidation.- is called oxidative phosphorylation.

Respiratory control

It is important for your body to control mitochondrial electron transport because it is a process by which you burn up (oxidize) nutrients.You don't want to burn up nutrients when you have little demand for energy. On the other hand, you would like to have plenty of energy available when you need it.A process that speeds up or slows down electron transport depending on energy demands is called respiratory control.

How might changes in the utilization of ATP speed up or slow down electron transport?

When a large PMF is generated by slowing the ATP synthase, there is not enough energy in electron transport to transport more protons across the membrane.

Aerobic and Anaerobic respiration

All eukaryotes and many prokaryotes use oxygen as the final electron acceptor in aerobic respirationSome prokaryotes, especially those in oxygen-poor environments, use other electron acceptors in anaerobic respiration.

Oxygen as a final electron acceptor

Oxygen is the most effective electron acceptor because:1. It is a strong electron acceptor2. A large difference between the potential energy of NADH and O2 electronsCells that do not use oxygen as an electron acceptor:1. Cannot generate such a large potential energy difference2. Make less ATP than cells that use aerobic respiration.

Fermentation

-Does not require O2-Involves glycolysis and the Regeneration of NAD+.-Occurs when pyruvate or a molecule derived from pyruvate accepts electrons from NADH-This transfer of electrons oxidizes NADH to NAD+.-Glycolysis can continue to product ATP via substrate-level phosphorylation.

Different Fermentation pathways: in Lactic acid fermentation

In lactic acid fermentation:-Pyruvate produced by glycolysis-accepts electrons from NADH-Lactate and NAD+ are produced--Lactic acid fermentation occurs in muscle cells.

Different Fermentation pathways: in alcohol fermentation

In alcohol fermentation-Pyruvate is enzymatically converted to acetaldehyde and CO2.-Acetaldehyde accepts electrons from NADH.-Ethanol and NAD+ are produced--Alcohol fermentation occurs in yeast

Fermentation efficiency

Fermentation is extremely inefficient, compared to cellular respiration.Produces just two ATP molecules per glucose molecule, while cellular respiration produced about 29 ATP molecules per glucose molecule.Organisms never use fermentation if an appropriate electron acceptor is available for cellular respiration.

Photosynthesis overview

The process of using sunlight to produce carbohydrates.Solar energy is converted and stored in the chemical bonds of carbohydrates.Requires sunlight, carbon dioxide, and water.Produced oxygen as a by-product.

Chloroplasts

photosynthesis occurs in the chloroplasts of green plants, algae, and other photosynthetic organisms.Chloroplasts are surrounded by two outer membranesIn plants, cells that photosynthesize typically have 40-50 chloroplasts.

chloroplast structure

Internal membrane system of chloroplasts composed of flattened, vesicle-like structures called thylakoid membranes.Thylakoids form stacks called grana.Thylakoid membranes contain photosynthetic pigments, such as chlorophyll.Fluid-filled space between the thylakoids and the inner membrane is the stroma.

Photosynthesis reaction

Photosynthesis contrasts with cellular respiration.Photosynthesis is endergonic, reducing CO2 to sugar (ΔG= +686 kcal/mol).Cellular respiration is exergonic, oxidizing sugar to CO2.

Light and Dark reactions

There are two kinds of reactions in photosynthesis.

Light reactions

Make ATP and NADPH which are used in dark reactions.Produce O2 from H2O.

Dark reactions (Calvin cycle reactions)

Also known as Calvin cycle reactions, reduce CO2 to produce sugars.

Where do light and dark reactions occur?

Light reactions occur in the thylakoid membranes.Dark reactions occur in the stroma.

Light

-- As a particle, light exists in discrete packets as photons.-- As a wave, light can be characterized by its wavelength.Each photon and wavelength have a specific amount of energy.The energy of a photon of light is inversely proportional to its wavelength.

Photosynthetic pigments absorb light

Pigments are molecules that absorb certain wavelengths of light.There are two major classes of pigments in plant leaves:1. Chlorophylls (chlorophyll a and chlorophyll b)2. CarotenoidsEach pigment has a specific absorption spectrum-- Wavelengths of light absorbed by a pigmentPhotosynthesis also has an action spectrum-- Shows the rate of photosynthesis at different light wavelengths

Absorption and Action spectra

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What wavelengths of light would be best for growing plants?

Blue and red light

What do light reactions produce that dark reactions use?

NADPH and ATP

Chlorophyll

Have a long "tail" made of isoprene subunits.-- Keeps the molecule embedded in the thylakoid membraneA "head" consisting of a large porphyrin ring with a magnesium atom in the middle-- Light is absorbed in the porphyrin ring.

Carotenoids and other accessory pigments

Carotenoids are accessory pigments that absorb light. They pass the energy on to chlorophyll.Classified into two groups: carotenes and xanthophyllsAbsorbs wavelengths of light not absorbed by chlorophyll.-- Extend the range of wavelengths that can drive photosynthesis

Photosystems

Chlorophyll molecules act collectively in groups of molecules to capture light-- They form complexes called photosystems.A photosystem consists of two major elements:1. An antenna complex of light harvesting chlorophylls2. A reaction center

The antenna complex

The antenna complex is composed of chlorophyll and carotene molecules that gather light.When a photon is absorbed by a pigment in the antenna complex, an electron is excited to a higher energy level.This energy is passed from one chlorophyll molecule to another by resonance energy transfer until it reaches the reaction center.

the reaction center

Consists of a specialized chlorophyll molecule which boosts an electron up to an electron acceptor with a higher reducing potential.

Photosystems I and II

There are two types of photosystems in green plants:1. Photosystem I (PSI) -P700 reaction center2. Photosystem II (PSII) -P680 reaction center

The Z scheme

A model for how photosystems I and II act together is called the Z scheme.The photosystems are connected in series to boost electrons to higher reducing potential

Photosystem II

-Splits water into O2 and H+ to obtain electrons for photosynthetic electron transport-Reaction center chlorophyll (P680) boosts the electron up to reduce the electron acceptor pheophytin-A pigment molecule structurally similar to chlorophyll

Between photosystem II and I

Electrons are passed down from the pheophytin through carriers in the electron transport chainProducing a proton gradient (PMF)Driving ATP production via ATP synthase

Photosystem I

Antenna chlorophylls Absorb photons and pass energy to reaction centersElectrons from PSII are boosted to higher reducing potential and then passed down an electron transport chain to ferredoxin, finally to reduce NADP+ to NADPH.

What do most of the chlorophyll molecules in a photosystem do?

Gather light energy.

Summary of PSI and PSII

Photosystem ii splits water and drives electrons from water to higher reducing potential.The e- transport chain between a proton gradient that drives the synthesis of ATPPhotosystem I yields reducing power in the form of NADPH.Several groups of bacteria have just one of the two photosystems.The cyanobacteria, algae, and plants have both.

Recap of the Z scheme

A photon excites an electron in a chlorophyll of photosystem II antenna complex.This excitation energy is transferred by resonance energy transfer from chlorophyll until it reaches the reaction center chlorophyll (P680)The reaction center chlorophyll, P680, transfers an excited electron to pheophytin. The electrons of photosystem II are replaced by electrons stripped from water, producing oxygen gas.From pheophytin, the potential energy of the electron is gradually stepped down through redox reactions in an electron transport chain.Plastoquinone uses the released energy to transport protons across the thylakoid membrane and build up a proton motive force (PMF) to make ATP.At the end of the electron transport chain from photosystem II, is a protein called plastocyanin (PC), which donates the electron to photosystem I linking the two photosystems.Excitation energy from the photosystem I antenna is transferred to the reaction center chlorophyll, P700.Electrons from P700 are boosted to an electron receptor and replaced by those from plastocyanin.Electrons from the electron receptor are passed down the electron transport chain through ferredoxin to NADP reductase, which are used to reduce NADP+ to NADPH.

In the Z-scheme of photosynthesis....

A.) The energy dissipated between photosystem II and I is captured in ATP synthesisB.) Connects photosystems in seriesC.) Uses P680 as the reaction center in PSII and P700 in PSID.) All of the above

The enhancement effect

The Z scheme results in an enhancement effect.Photosynthesis is more efficient when:- illuminated by light at both 680 nm and 700 nm wavelengths- activating both photosystems

Dark reactions: CO2 fixation and the Calvin cycle

Light reactions produce ATP and NADPH.These products are used to dive the dark cycle reactions:- CO2 fixation and the Calvin cycle-Which take place in the stroma of chloroplasts

The Calvin cycle

**special attention to Rubisco

The importance of Rubisco

Rubisco is a CO2-fixing enzyme, also known as Ribulose 1,5-biphosphate carboxylase/oxygenase.Rubisco is the primary enzyme used to fix CO2 in C3 plants.Rubisco is the most abundant enzyme on Earth.It is inefficient in catalyzing the addition of CO2 to RuBP because it also catalyzes the addition of O2 to RuBP.

Photorespiration

O2 and CO2 compete at the active sites of Rubisco, which slows the rate of CO2 production in a process called photorespiration.

Photorespiration continued...

Photorespiration "undoes" photosynthesis. It consumes energy and releases fixed CO2.Photorespiration is most problematic when CO2 levels are low, O2 levels are high, and temperature is high.Photosynthesis (on the left) is also known as the Calvin cycle.***

Stomata basics

Leaf structures where gas exchange occurs. Consist of two guard cells that change shape to open or close.

Stomata

During photosynthesis in a leaf, the CO2 concentration falls as free CO2 is fixed into carbon compounds.Stomata open to allow entry of more CO2 and exit of O2. However, Water is also lost when stomata are open.

Conditions favoring photorespiration

In hot, dry weather, leaf cells close their stomata to prevent water loss and dehydration. Under these conditions, CO2 levels decline and O2 levels rise favoring photorespiration.

C4 Photosynthesis

Plants in warm, dry climates have evolved C4 photosynthesis to deal with the problem of photorespiration.C4 photosynthesis limits photorespiration by spatially separating carbon fixation from the Calvin cycle.Carbon fixation occurs in mesophyll cells, Calvin cycle occurs in adjacent bundle sheath cells.

How C4 photosynthesis works

In C4 plants, a different enzyme, not subject to photorespiration, PEP carboxylase fixes CO2 in mesophyll cells. CO2 fixation produces a 4-carbon compound which is transported to bundle-sheath cells.In bundle sheath cells, the 4 carbon compound breaks down and releases CO2. Rubisco fixes the CO2 into the Calvin cycle.

C4 compared to C3 photosynthesis

C4 plants:Enzyme is PEP carboxylase3-carbon compound+CO2-->4 carbon organic acidsC3 plants:Enzyme is RubiscoRuBP+CO2-->2 3-phosphoglycerate (2-carbon sugar)

In C4 plants...

A four carbon compound is transferred from mesophyll to bundle sheath cells

What are CAM plants?

In plants that fix CO2 utilizing crassulacean acid metabolism (CAM):- Carbon fixation and the Calvin cycle are separated in time-Also live in hot, dry habitats-Keep their stomata closed all day-Open them only at night

CAM plants

During the night, CAM plants take in CO2 and temporarily fix it into organic acids.During the day, CO2 is released from the stored organic acids. Used by the Calvin cycle to minimize photorespiration.

C4 and CAM photosynthesis

C4 photosynthesis and CAM function as CO2 pumpsThey minimize photorespiration when:-stomata are closed-CO2 cannot diffuse in directly from the atmosphereIn C4 plants the reactions catalyzed by PEP carboxylase and Rubisco and separated in space.In CAM plants, the reactions are separated in time.

The regulation of photosynthesis

The rate of photosynthesis is finely tuned to reflect changes in environmental conditions and to use resources efficiently.For example, light triggers synthesis of photosynthetic proteins. High sugar levels inhibit synthesis of photosynthetic proteins.

Carbon cycle

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Mitosis

Is the cell division process involved in the propagation of somatic cells.Distributes replicated chromosomes to daughter cells.

M phase and Interphase

Growing cells cycle between two phases:1. A dividing phase called mitosis or M phase2. A nondividing phase called interphase.Interphase is further subdivided into three subphases: Gap1 (G1), S phase (S), and G2 Phase (G2).

Determining the time spent in each phase

The length of the whole cell cycle can be inferred from the doubling time of cells in culture.For mammalian cells, it is usually about 24 hours.

Determining the length of M phase

Fraction of cells in mitosis (mitotic index) relates to the fraction of the cell cycle that cells spend in mitosis.

If the cell cycle for onion cells is 24 hours and 10% of the cells are in mitosis when you peer into a microscope, about how long is M phase?

2.4 hoursSolution 10% of the cells in M phase indicates that 10% of the cell cycle is spent in S phase.24 hr x 0.10 = 2.4 hr

S phase

Chromosome replication occurs during synthesis (S) phase. It can be demonstrated by the incorporation of Bromodeoxyuridine (BrdU) into DNA, a synthetic nucleoside.BrdU can be detected by an antibody tagged with a dye.

Detection of cells undergoing DNA synthesis using BrdU

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Time spent in S phase

Fraction of cells at any one time in S phase relates to the fraction of time in the cell cycle that cells spend in S phase.Example: 15/60 or 25% of the cells in S-phase indicates that 25% of the cell cycle is spent in s phase.24 hr x 0.25 = 6.25 hr

Interphase: Gap phases

Interphase also includes phases before and after DNA synthesis.G1 phase occurs before the S phase.G2 phase occurs after S phase and before mitosis.During the gap phases, cells grow, particularly during G1.

You observe that a population of cells in culture double every 48hrs and 10% of the cells are in mitosis when you peer at the cells through a microscope.You conduct a BrdU labeling experiment and find that about half of the cells are labeled with BrdU at any one time.By adding a cancer therapeutic drug, you are able to block cells at the beginning of S phase. However, the drug is reversible and when you remove it, the cells enter mitosis 30 hrs later. From that you deduce that G2 is about 6 hrs long.How was it concluded that G2 is 6hr long? From this information, what is your estimate for the length of G1?

Length of cell cycle=48 hrLength of M phase= 48hr x 0.1 =4.8 hrLength of S phase = 48hr x 0.5 =24 hrsLength of G2= 30hr-length of S phaseLength of G2= 30 hr-24hr=6hrG1 = length of cell cycle - (S + G2 +M)G1= 48 hr - (24+6+~5hr)= 48-35hr=13 hr

Chromosome replication

Chromosomes are replicated in S phase during each round of the cell cycle to produce Sister chromatids.An unreplicated chromosome consists of a single chromatid (one double helix of DNA)A replicated chromosome consists of two sister chromatids (two double helices of DNA).Mitosis distributes sister chromatids (chromosomes) to daughter cells during cell division.In mitosis, chromosomes condense into compact structures that can be moved around the cell.

Chromosome segregation events in mitosis

During mitosis:- sister chromatids separate to form independent chromosomes.-Each daughter cell receives a copy of the genetic information contained in each chromatid (chromosome).

Phases of mitosis

1. Prophase2. Prometaphase3. Metaphase4. Anaphase5. Telophase

Interphase

After chromosome replication, each chromosome is composed of two sister chromatids.

Prophase

Chromosomes condense, and spindle apparatus begins to form.

Prometaphase

Nuclear envelope breaks down, Microtubules contact kinetochores.

Metaphase

Chromosomes complete migration to middle of cell.

Anaphase

Sister chromatids separate into daughter chromosomes and are pulled apart.

Telophase

The nuclear envelope re-forms, and chromosomes de-condense.

Cell division begins

Actin-myosin ring causes the plasma membrane to begin pinching in.

Cell division is complete

two daughter cells form

mitotic spindle

Made up of microtubules called spindle fibers.Polar microtubules push the poles of the cell away from each other during mitosis.Kinetochore microtubules connect to chromosomes and draw them to the poles during mitosis.Polar microtubules move by sliding past each other driven by motor proteins (kinesins) that power the sliding.Kinetochore microtubules move by disassembly.

microtubule assembly

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Research Question: How do kinetochore microtubules shorten to pull daughter chromosomes apart during anaphase?

Hypothesis: Microtubules shorten at the spindle pole.Alternative hypothesis: Microtubules shorten at the kinetochore.Experimental setup: 1. Apply fluorescent labels2. bleach a section of microtubules with a laserResults: The darkened areas of the microtubules remained stationary as the chromosomes moved through them toward the pole.Conclusion: Kinetochore microtubules shorten at the kinetochore to pull daughter chromosomes apart during anaphase.

How do chromosomes move during mitosis?

Kinetochore microtubules remain stationary during anaphase. They shorten because tubulin subunits of the microtubules dissemble from their plus ends at the kinetochore.

Cytokinesis in animal cells

Cytokinesis in animals, fungi, and slime molds occurs when a ring of actin and myosin filaments contracts inside the cell membrane, causing it to pinch inward in a cleavage furrow.

Cytokinesis in plant cells

Cytokinesis in plants occurs as vesicles are directed by microtubules from the Golgi apparatus to the middle of the dividing cell. These vesicles fuse to form a cell plate.

Control of the cell cycle

Length of the cell varies greatly among cell types. Variation in the length of G1 phase accounts for differences.G1 phase is virtually eliminated in rapidly dividing cells.Nondividing cells stop in the G1 stage called G0.

Mitosis-Promoting factor

Mitosis-promoting factor (MPF) induces mitosis. It is present in the cytoplasm of M-phase cells.MPF is composed of two distinct subunits.--A Cyclin-dependent protein kinase (CdK) and a cyclin*The protein kinase is an enzyme that catalyzes the transfer of a phosphate group from ATP to a target protein (phosphorylation)The cyclin subunit functions as a regulatory protein that activates CdK

Cyclin levels regulate MPF

Cyclin levels increase during interphase, peak in M phase before decreasing again. CdK levels remain constant.When cyclin levels are high, more MPF is active. The target proteins are phosphorylated, initiating mitosis.

MPF deactivation

During anaphase, an enzyme complex begins degrading MPF's cyclin subunit.MPF triggers events that leads to its own destruction.

During the cell cycle the activity of MPF rises and falls...

Driven by changes in the levels of cyclin.

Cell-cycle checkpoints

There are 3 checkpoints. Each checkpoint allows a cell to "decide" whether to proceed.

G1 checkpoint

First and most important checkpoint occurs late in G1.Four factors affect whether cells pass the G1 checkpoint:1. cell size2. Nutrient availability3. Social signals from other cells4. Integrity of DNA

What happens if DNA is damaged at the G1 checkpoint?

If DNA is physically damaged, a protein called P53 pauses the cell cycle OR initiates apoptosis, a programmed cell death.P53 is an example of a tumor suppressor. Failure of P53 to act can lead to uncontrolled cell division.

G2 checkpoint

The second checkpoint is between the G2 and M phases.Cells stop growing here if chromosome replication is not complete OR is DNA is damaged.

Metaphase checkpoint

Third checkpoint, during M phase. Cell cycle progress ceases during metaphase if the chromosomes are not properly attached to the mitotic spindle.This mechanism prevents incorrect chromosome separation and also prevents giving daughter cells the wrong number of chromosomes.

Cancer

Complex family of diseases caused by cells that grow in an uncontrolled fashion, invade nearby tissues, and spread to other sites in the body.Cancers arise from cells in which cell-cycle checkpoints have failed.

tumor

forms when cells divide in an uncontrolled fashion

benign tumors

noninvasive and noncancerous

malignant tumors

are invasive and spread throughout the body via the blood or lymph; can initiate secondary tumors.

metastasis

when cancer cells detach from the original tumor and invade other tissues.

types of cancerous cell defects

two types of defects:1. Defects that make the proteins required for cell growth active when they should not be2. Defects that prevent tumor suppressor genes from shutting down the cell cycle

Newer cancer therapies

1. Checkpoint inhibitors inhibit the checkpoint for damaged DNA. Following radiation treatment, it allows tumor cells to progress in the cell cycle with damaged DNA. Tumor cells with damaged DNA undergo programmed cell death.2. Immunotherapies stimulate the immune system to attack cancer cells. Monoclonal antibodies directly target cancer cell antigens.

apoptosis

Programmed cell death

History of gene research

Early researchers knew that chromosomes were comprised of DNA and protein. However, they did not know whether genes in chromosomes were composed of DNA or protein.The general consensus at the time supported the hypothesis that genes were made of proteins because of the relative complexity and variability of proteins. Comparison to DNA, which is comprised of only four different nucleotides.

Hershey-Chase experiment

Alfred Hershey and Martha Chase conducted the first experiments in 1952 to determine whether genes were DNA or protein.They studied a virus (bacteriophage) called T2 that infects the bacterium E. coli.The viruses are made of DNA and protein.T2 infection of E. coli begins when the virus attaches to the cell and injects its genes into the cell. The material injected is considered to be genetic material because it directs the production of new virus particles.During infection, the protein coat, or capsid, of the original parents virus is left behind as a ghost attached to the exterior of the cell.Hershey and Chase grew the virus in the presence of one of two radioactive isotopes: 32P to label DNA OR 35S to label proteins.Labeled viruses were used to infect E. coli cells.They hypothesized that if genes consist of DNA, then the 32P-labeled DNA would be found inside the cells, while 35S-labeled proteins would be found only in the ghosts outside the cells.Results: 32P-labeled DNA was found in the cell pellet and 35S-labeled protein was found in the viral capsids (ghosts) in solution.This result supports the proposal that genes are made of DNA, not protein.

capsid

Outer protein coat of a virus

Watson and Crick

solved the structure of DNA in 1953-- double strand helical structure.

DNA structure

Each single strand of DNA is made of:1. A backbone of sugar (deoxyribose) and phosphate groups.2. Nitrogen-containing bases (A,C,G,T) that project from the backbone.3. The individual repeating units are called deoxyribonucleotides.DNA strands have directionality. One end has an exposed hydroxyl group on the 3' carbon of deoxyribose. The other end has an exposed phosphate group on a 5' carbon.Thus, the molecule has a 3' end and a 5' end.Refer to chapter 15 slides for better pictures

DNA secondary structure

Watson and Crick proposed that the DNA strands run antiparallel to each other (in opposite directions.)The helical structure is stabilized by base pairing involving hydrogen bonds.Adenine (A) hydrogen bonds with with thymine (T)Guanine (G) hydrogen bonds with cytosine (C).Because of base pairing, one strand is a complement of the other strand.

DNA strands are templates for DNA synthesis

Watson and Crick also proposed that the existing strands of DNA served as a template (pattern) for the production of new strands. Bases were added to the new strands according to complementary base pairing.Three alternative hypotheses for how the DNA is replicated:1. Conservative replication2. Semiconservative replication3. Dispersive replication

DNA replication hypothesis: Conservative replication

The parental molecule serves as a template for the synthesis of an entirely new double stranded molecule.

DNA replication hypothesis: Semiconservative replication

The parental DNA strands separate, and each is used as a template for the synthesis of a new daughter strand.DNA molecules each consist of one old parental and one new daughter strand.

DNA replication hypothesis: Dispersive replication

The parent molecule is replicated in sections.The replicated molecules contain old DNA interspersed with newly synthesized DNA.

Meselson-Stahl experiment

Mathew Meselson and Frank Stahl designed an experiment to determine the mode of DNA synthesis.They grew E. Coli in the presence of "heavy" nitrogen (15N) to label the bacteria's DNA. Then they moved the bacteria to a normal 14N- containing medium.They then analyzed DNA by density at different times after shift to 14N. Results from the experiment are consistent with the hypothesis for semiconservative DNA synthesis.

DNA Synthesis

DNA is synthesized by an enzyme called DNA polymerase.DNA synthesis involves the incorporation of deoxyribonucleoside triphosphates (dNTPs) into DNA.DNA synthesis is exergonic because the high energy phosphate bonds are hydrolyzed in the reaction.

Characteristics of DNA Polymerases

DNA polymerases can only polymerize a new strand in one direction!DNA polymerases can only add dNTP's to the 3' end of a growing DNA chain. Thats because the only reaction catalyzed by DNA polymerase is nucleophilic attack of the 3'OH on the alpha-phosphate of the incoming dNTP.

Phosphodiester bonds

The polymerization reaction leads to the formation of a phosphodiester bond between polymerized nucleotides.

Base pairing rules

The incoming nucleotide is incorporated according to base pairing rules.

How does DNA replication start?

DNA has to unwind locally during DNA replication to separate DNA strands.A replication bubble forms at the origin of replication. It grows in both directions with a replication fork at each end of the bubble.

Origin of replication

In bacterial chromosomes, the replication process begins at a single origin of replication. It then proceeds in both directions (bidirectional replication)

Eukaryotes- DNA replication

Eukaryotes also have bidirectional replication, but they have multiple origins of replication on a single chromosome. Plus, they have more than one (often many) chromosomes.

Eukaryotic chromosomes have multiple origins of replication because they have so much DNA per chromosome. If a typical human chromosome has a single bidirectional replication bubble (starting at the middle of the chromosome), how long (in hours) would it take to replicate the chromosome based on the following information?:Typical human chromosome= 150 x 10^6 bp of DNARate of deoxynucleotide incorporation at a single replication fork = 50 bp/sec

50 bp/sec/replication fork x2 replication forks = 100 bp/sec150 x 10^6 bp/100 bp/sec = 1.5 x 10^6 sec1.5 x 10^6 sec/3.6 x 10^3 sec/hr = 416 hr (~17 days)

How is the helix opened?

Several proteins are responsible for opening and stabilizing the DNA double helix in the replication bubble:1. Enzyme helicase catalyzes the breaking of hydrogen bonds to separate the two DNA strands.2. Single-strand DNA-binding proteins (SSBPs) keep the strands separated.Unwinding the DNA helix creates tension farther down the helix.Enzyme topoisomerase cuts and rejoins the DNA downstream of the replication fork relieving tension in the helix.

The replication fork

A problem at the replication fork: Recall that DNA can only be synthesized in one direction. One strand is synthesized in the direction of movement of the fork, while the other is not.Strands synthesized in the direction of the fork are called the leading strands.Strands synthesized in the opposite direction are called the lagging strands.

Leading and lagging strands

The leading strand is synthesized in a continuous manner.The lagging strand is synthesized in a discontinuous manner, as short pieces of DNA called Okazaki fragments have to be initiated over and over again.

Initiation of DNA synthesis

DNA polymerase requires a primer to initiate DNA synthesis.A primer is a small oligonucleotide bonded to the template strand. It provides a free 3' hydroxyl (OH) group that forms a phosphodiester bond with an incoming dNTP.

Primase

Synthesizes a short RNA segment that serves as a primer. DNA polymerase III then adds bases to the 3' end of the primer.

How is the lagging strand synthesized?

Primase synthesizes a short RNA primer.DNA polymerase III adds bases to the 3' end of the primer forming an Okazaki fragment.*Another Okazaki fragment is synthesized.DNA polymerase I removes the RNA primer at the beginning of each Okazaki fragment and fills the gap.DNA ligase joins the Okazaki fragments to form a continuous DNA strand.

DNA synthesis machine

Replisome is a large, multi-enzyme machine responsible for DNA synthesis at the replication fork.

Replicating the ends of linear chromosomes

Telomeres are the regions at the ends of linear chromosomes. They consist of short, Repeating stretches of bases. They do not contain genes. The replication fork reaches the end of a linear chromosome and can't prime on the end of the lagging DNA strand.The enzyme telomerase adds more repeating bases to the end of the lagging strand, catalyzing the synthesis of DNA from an RNA template carried with it.Primase then makes an RNA primer. DNA polymerase uses primer to synthesize the lagging strand.Ligase connects the new sequence and prevents the lagging strand from shortening.

Errors in DNA replication

DNA replication is very accurate-- average error rate of less than one mistake per billion cases.DNA polymerization inserts an incorrect base only about once every 100,000 bases.How is the difference between DNA replication and DNA polymerization made up?

DNA polymerase proofreading

DNA polymerase can also proofread its work.If the enzyme finds a mismatch, it pauses and removes the mismatched base that was just added. Proofreading reduced the error rate to about 1 x 10^-7

Mismatch pair

Further repair of misincorporated bases occurs after DNA synthesis. This process is called mismatch repair.It replaces a mismatched base with the correct base. It reduces the error rate even further to one in a billion cases (1 x 10^-9)

Repairing damaged DNA

DNA can be broken or altered by various chemicals or radiation.UV light can cause thymine dimers to form. These dimer produce a kink in the DNA strand.The nucleotide excision repair system recognizes DNA damage such as thymine dimers. Enzymes then remove the single-stranded DNA in the damaged section.The complementary DNA strand provides a template for resynthesis of the defective sequences.

Why is the lagging strand synthesized in Okazaki fragments?

Because DNA polymerase has to start over and over to keep up with the replication fork.

What problem is encountered in replicating DNA at the ends of chromosomes (telomeres)?

Run out of template to prime DNA synthesis on the lagging strand

What is the difference between DNA polymerase proofreading and excision repair?

1. Proofreading happens during DNA synthesis2. Proofreading generally replaces a single mismatched base3. Excision repair may excise a segment of damaged DNA.

Okazaki fragments

Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.

Gene expression

the process of converting the information in DNA into functions within the cell.

What do genes do?

George Beadle and Edward Tatum proposed that the function of a gene could be determined by knocking it out.They created mutants by irradiating the bread mold, Neurospora crassa. One mutant lacked an enzyme to make *pyridoxine (vit B6).The mutation occurred in only one gene.Observation inspired them to hypothesize that one gene makes one protein (enzyme).

One-Gene, One-Enzyme Hypothesis

Adrian Srb and Norman Horowitz further tested the one-gene, one-enzyme hypothesis in Neurospora. They examined the production of the amino acid arginine.Arginine is produced via a metabolic pathway, requiring the action of three different enzymes. They hypothesized that different genes lead to the synthesis of each of the three enzymes.To test their hypothesis, Srb and Horowitz used radiation to create thousands of mutants. They then performed a genetic screen to select mutants incapable of producing arginine.To identify the enzyme (and hence the gene) affected in any particular mutant, they pinpointed the block in the arginine metabolic pathway.One mutant would grow in medium supplemented with Citrulline or Arginine, but would not grow on medium supplemented with Ornithine.The mutant also tended to accumulate Ornithine.

Francis Crick

proposed that DNA is the source of information for the synthesis of proteins; the sequence of bases in DNA is a code; and different combinations of bases in DNA specify the sequence of amino acids in a protein.The information encoded in DNA is not directly translated into the amino acid sequence of proteins.

The Central Dogma

Proposed by Francis Crick, explains that DNA codes for RNA, which codes for proteins.According to the central dogma, an organism's genotype is determined by the sequence of bases in its DNA (genes); and an organism's phenotype is a product of the proteins it produces.DNA= nucleotidemRNA=nucleotideProtein=amino acids

RNA- Links genes to proteins

François Jacob and Jaques Monod proposed: that RNA molecules link genes found in the nucleus to the manufacture of proteins in the cytoplasm.* Messenger RNA (mRNA) was found to carry information from DNA to the site of protein synthesis.The enzyme RNA polymerase synthesizes RNA according to the information provided by the sequence of bases in DNA.

The Central Dogma (picture)

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Modern exceptions to the Central Dogma

Certain viruses can turn RNA into DNA.DNA also encodes "noncoding RNA" that does not make protein but regulates other genes.

The genetic code

The genetic code had information encrypted for the synthesis of specific proteins.George Gamow predicted each word in the genetic code contains three bases.There are 20 amino acids but only four different RNA bases.A three-base code could code for 4^3 = 64 different amino acidsA three-base code provides more than enough information to code for all 20 amino acids.

George Gamow

predicted each word in the genetic code contains three bases.

Triplet code

A three-base code is known as a triplet code.A codon is a group of three bases that specifies a particular amino acid.The triplet code is redundant. Some amino acids are specified by more than one codon.

A codon

Is a group of three bases that specifies a particular amino acid.

DNA code vs RNA code

in the RNA code U substitutes for T, but still pairs with A.

Cracking the code

Marshall Nirenberg and Philip Leder deciphered the genetic code by determining which of the 64 codons coded for each for the 20 animo acids.There is one start codon (AUG). It signifies that *start of the protein-encoding sequence in mRNA.There are three Stop codons(UGA, UAA, and UAG) in the genetic code which signal the end of the protein-coding sequence.

Start codon(s)

AUG

Stop codon(s)

UGA, UAA, UAG

The genetic code

It is redundant. All amino acids except two are encoded by more than one codon.It is unambiguous. One codon never codes for more than one amino acid.It is nearly universal. All codons specify the same amino acids in all organism (with a minor exceptions.)It is conservative. The first two bases are usually identical when multiple codons specify the same animo acid.

Predicting an amino acid sequence

Watch a video

Point mutations

Point mutation is a change in a Single DNA base. It can occur when DNA polymerase inserts the wrong base into the newly synthesized strand of DNA if the DNA polymerase proofreading and mismatch repair systems fail.Point mutations may be:Missense mutations: change the amino acid sequence of the encoded proteinSilent mutations: do not change the animo acid sequence of the gene product

Missense mutations

change the amino acid sequence of the encoded protein

Silent mutations

do not change the animo acid sequence of the gene product

Nonsense mutations

prematurely terminate a protein

Frameshift mutation

addition or deletion of bases shifts the reading frame

Mutations have varying effects

1. Beneficial mutations increase the fitness of the organism.2. Neutral mutations do not affect an organisms fitness. (Silent mutations are usually neutral)3. Deleterious mutations decrease the fitness of the organism.Most mutations are neutral or slightly deleterious.

Imagine a block on gene 3. What would you predict for a mutation in gene 3?

Growth on Arginine

Recently scientists have developed two new bases that can be incorporated into DNA and that base pair with each other-- bringing the total number of DNA bases to six. If a new code was developed for such DNA, how many bases would be needed in a codon to code for all 20 amino acids?

Two (a doublet)A three-base code with 4 nucleotides could code for 4^3 = 64 different amino acids.A two-base code with 6 nucleotides could code for 6^2 = 36 different amino acids.

What type of mutation does this represent?UAC --> UCC

Missense

Transcription

The first step in converting genetic information into proteins is transcription, which is synthesis of a mRNA from DNA by RNA polymerase.RNA differs from DNA in that RNA is single stranded and in which Uracil (U) substitutes for thymine (T).

Overview of transcription

RNA polymerase transcribes only one strand of DNA called the template strand.The other DNA strand is the non-template, or coding strand.

Characteristics of RNA Polymerase

Like DNA polymerase, RNA polymerase synthesizes RNA in the 5'-to-3' direction.Unlike DNA polymerases, RNA polymerases do not require a primer to begin transcription.Bacteria have one RNA polymerase type.Eukaryotes have three or more types: RNA polymerase I, II, and III.

Transcription Initiation in prokaryotes

First phase of transcription is gene initiation.RNA polymerase cannot find the transcription start site or initiate transcription on its own; it requires other factors.A factor called "Stigma" is required for the initiation of RNA synthesis in prokaryotes. It binds to RNA polymerase.

What role does Stigma play in initiation?

Prokaryotic RNA polymerase is made up of the core enzyme and a stigma subunit.Stigma acts as a regulatory subunit of RNA polymerase guiding it to specific promotor sequences on the DNA template strand.

Bacterial promoters

Promoters are regions of DNA that control the expression of a gene and lie immediately upstream from the gene. They are:40-50 base pairs longHave two key regions: -10 box and -35 box...The -10 box consists of the sequence TATAAT.The -35 box consists of the sequence TTGACA.

Stigma initiates transcription

Stigma, and not RNA polymerase, makes the initial contact with the promoter. Transcription starts immediately downstream from the promoter at the transcription start site.Most bacteria have Several types of Stigma factors. Each allows RNA polymerase to bind to a different type of promoter.E. coli has ~4,300 genes, but only 7 different Stigma factors.

Transcriptional initiation

Stigma opens the DNA double helix. The template strand is threaded through the RNA polymerase active site.An incoming ribonucleoside triphosphate (RTP) pairs with a complementary base on the DNA template strand. RNA polymerization begins.

Elongation and termination

During the elongation phase of transcription, RNA polymerase moves along the DNA template. It synthesized ENA in the 5'-to-3' direction.Transcription ends with a termination phase. RNA polymerase transcribes a transcription termination signal.

Transcriptional termination

In bacteria, the transcription termination signal codes for RNA that forms a hairpin structure. It causes the RNA polymerase to separate from the RNA transcript, ending transcription.

Eukaryotic promoters

Eukaryotes have more diverse, longer, and more complex promoters than do prokaryotes.Many of the eukaryotic promoters include:-A TATA box about 30 base pairs upstream of the +1 that binds basal transcription factors.-Enhancer elements that bind specific transcription factors called activators.-Silencer elements that find specific transcription factors called repressors.-Coactivators mediate the interaction between the basal and specific transcription factors.

Transcription initiation in eukaryotes

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Introns

Eukaryotic genes are interrupted by introns, regions of genes that are non-coding and are not present in the mature mRNA.Transcription of these genes gives rise to a pre-mRNA which must be processed to remove introns.

Exons

Exons are the coding regions of eukaryotic genes, and will be part of the final mRNA product.

RNA splicing

Introns are removed by RNA splicing mediated by splicesomes in cell nuclei.Splicesomes are complexes composed of small nuclear ribonucleoproteins (snRNPs)

If introns are removed from mRNAs by splicing, then why do genes in eukaryotes have introns?

1. Allow for alternative splicing (greater protein diversity)2. Promote more genetic recombination (exon shuffling)3. May be evolutionary remnants4. Derived from transposable elements5. Slows transcription (makes for longer genes)6. Provides for tight regulatory switchesNot buffers or inhibitors--not to keep exons from running together or overlapping.

Caps and tails

RNA transcripts in eukaryotes are also processed by the addition of a 5' cap and a poly(A) tailRNA processing is complete upon:-addition of the cap which is recognized by the translation of machinery-addition of the poly(A) tail which protects the mRNA from degradation.

Transcription and translation in bacteria

In bacteria, transcription and translation occur simultaneously.Bacterial ribosomes Can begin translating an mRNA before RNA polymerase has finished transcribing it. Multiple ribosomes on a mRNA form a polyribosome.

Transcription and translation in eukaryotes

In eukaryotes, transcription and translation are spatially and temporally separated.mRNAs are synthesized and processed in the nucleus; then transported to the cytoplasm for translation by ribosomes.

Stigma...

A.) Is a regulatory subunit of prokaryotic RNA polymeraseB.) Makes the initial contact with the promoter during the initiation of transcriptionC.) Binds to the -35 and -10 boxes in bacterial promotersD.) All of the above

Why do eukaryotes have more transcription factors (regulatory subunits) than prokaryotes?

Because eukaryotes have more genes that are controlled differently

General structure of a protein

A chain of amino acids joined by peptide bonds.There are 20 different amino acids.Direction of synthesis:N terminus --> C terminus

Ribosomes and the translation machinery

The translational machinery consists of:-Ribosomes (large and small subunits)-mRNA-Transfer RNAs with attached amino acids-Growing polypeptide chain

Importance of transfer RNA (tRNA)

Transfer RNAs convert the nucleic acid code into an amino acid sequence.The CCA sequence (reading 5' to 3') at the 3' end of each tRNA is the binding site for amino acids.The triplet on the loop at the opposite end is the anticodon that reads the mRNA by base-pairing with mRNA codons.

Aminoacyl tRNA synthetases

Amino acids are attached to tRNA by animoacyl tRNA synthetases. They "charge" tRNAs. A tRNA covalently linked to its corresponding amino acid is called an aminoacyl tRNA.There is a different aminoacyl tRNA synthetase for each of the 20* amino acids.There are one or more tRNAs that can be charged with the same amino acid.

How many different tRNAs?

There are 61 different codons (excluding stop codons), but only about 40 different tRNAs in most cells.To resolve this deficit, Francis Crick proposed the wobble hypothesis. This proposed that the anticodon of tRNAs can still bind successfully to a codon with a third position that requires a nonstandard base pairing, for example, G can pair with U as well as with C.This means that some tRNAs are able to base-pair with more than one codon.

Wobble hypothesis

Proposed that the anticodon of tRNAs can still bind successfully to a codon with a third position that requires a nonstandard base pairing, for example, G can pair with U as well as with C.This means that some tRNAs are able to base-pair with more than one codon.

General mechanism of translation

Ribosomes consist of:"large subunits where peptide bonds are formed and small subunits that bind mRNA.*tRNAs bind via their anticodons to three sites on the large subunit (APE)

APE" sites on the large subunit

The A site of the ribosome is the acceptor site for an aminoacyl tRNA.The P site is where a peptide bond forms.The E site is where the spent tRNAs exit the ribosome.

How does a ribosome synthesize proteins?

In a three-step sequence:1. An animoacyl tRNA carrying the correct anticodon for the mRNA codon enters the A site.2. A peptide pond forms between the amino acid on the aminoacyl tRNA in the A site and the growing polypeptide on the tRNA in the P site.3. The ribosome moves ahead three bases. All the tRNAs move down one position. The tRNA in the E site exits.

Phases of translation

Translation has three phases:1. Initiation2. Elongation3. Termination

Translation Initiation in prokaryotes

The initiation phase of translation:1. mRNA binds to the small subunit2. Initiator aminoacyl tRNA bearing N-formylmethionine (f-met) binds to the AUG start codon.3. The large ribosomal subunit binds placing the initiator tRNA at the P-site.

Translation Elongation

At the start of the elongation phase, the initiator tRNA is in the P site while the E and A sites are empty. An aminoacyl tRNA binds to the codon in the A site via base pairing between anticodon and codon.Peptide bonds form between amino acids on the tRNAs in the P and A sites.After peptide bond formation, the growing polypeptide on the tRNA in the P site is transferred to the tRNA in the A site.

Moving down the mRNA...

Translocation occurs when the ribosome moves down the mRNA 3 nucleotides.The tRNA attached to the growing protein moves into the P site.The A site is not available to accept a new aminoacyl tRNA for binding to the next codon.The discharged tRNA that was in the P site moves to the E site. If the E site is occupied, then the tRNA at the E site is ejected.

Polypeptide chain elongation- recap

A messenger RNA is read 5'-->3', a protein is synthesized N-->C.Remember, 5'-->3', N-->C!!https://www.youtube.com/watch?v=Ikq9AcBcohA

Translation termination

The termination phase starts when the A site encounters a stop codon. This causes a release factor to enter the A site.Release factors resemble tRNAs in size and shape, but do not carry an amino acid.*These factors catalyze hydrolysis of the bond linking the polypeptide chain to the tRNA in the P site.

True or False: There are as many different aminoacyl tRNA synthases as there are different tRNAs.

False

The first aminoacyl tRNA initiation protein synthesis is...

placed at the peptidyl (P) site

A peptide bond is formed between the growing polypeptide on the tRNA at the ________ and the amino acid on the incoming aminoacyl-tRNA at the _________.

P site; A site

Post-translational modifications

Most proteins go through an extensive series of processing steps called post-translational modification. A common modification is protein phosphorylation.Folding determines a protein's shape and therefore its function.Molecular chaperones protect the protein from aggregation during protein folding.

Regulation of gene expression

Organisms need to be able to change their pattern of gene expression to optimize growth or simply to survive under changing environmental conditions.

Transcriptional control of gene expression

Transcriptional control occurs when cells regulate mRNA production from Specific genes.Cells regulate transcription through proteins that regulate gene expression. They affect the binding of RNA polymerase to the promoters of certain target genes-- affecting the initiation of transcription.Response is slow, but efficient.DNA-->(police officer)-->mRNA-->protein-->activated protein

Post-transcriptional/translational control

Post-transcriptional control can occur by regulating mRNA degradation (RNA stability).Translational control can occur globally, by regulating the rate of *translation*, or by regulating the translationtranslationl control* can occur globally, by regulating the rate of *translation*, or by regulating the *translation* of certain mRNAs.DNA-->mRNA-->(police officer)-->protein-->activated protein

Post-translational control

Occurs when cells regulate the activity of a protein. Usually involves chemical modification off a protein, such as protein phosphorylation. It can be a very rapid response.DNA-->mRNA-->protein-->(police officer)-->activated protein

Stages for controlling gene expression

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Gene regulation in bacteria

The lactose operon (lac operon) in E. coli is a classic example of transcriptional control of gene expression.E.coli can regulate gene expression to grow on different nutrients. The lac operon is involved in regulating metabolism of the sugar, lactose.

lactose metabolism

E.coli can utilize lactose as a carbon source. To utilize lactose, it must be transported into the cell by the transporter, galactoside (lactose) permease.The enzyme B-galactosidase is needed to cleave lactose into metabolize glucose and galactose.

The lac operon

The B-galactosidase and lactose permease genes are coordinately regulated in the lac operon.The lac operon has a single promoter that transcribes all the genes together into one mRNA.An important regulatory sequence lies immediately downstream from the promoter called the Operator.Gene 1= lacZ, B-galactosidase geneGene 2= lacY, lactose permease geneGene 3= lacA, transacetylase gene

Lactose induces gene expression

Lactose acts as an inducer of the genes in the lac operon.Jaques Monod and François Jacob* discovered how a small molecule, lactose, could induce these genes.

Analysis of mutants

They did so by isolating and analyzing E. coli mutants that could not metabolize lactose.1. Started by generating a large number of mutants2. Used replica plating to find mutants that could not induce lactose metabolism.

Replica plating

1. Grow bacterial colonies on master plates containing a medium with nutrients2. Transfer cells to a piece of sterilized velvet3. Transfer cells to a replica plateLooked for colonies that could grow on nutrients on the master plate, but could not grow on lactose alone on the replica plate.

Lactose metabolism mutants

Jacob and Monod analyzed mutants that could *not* grow on lactose, i.e., could notnot and Monod analyzed *mutants* that could *not* grow on lactose, i.e., could *not* induce lactose metabolism.lacZ-mutants lack functional B-galactosidaselacY-mutants lack the membrane protein galactoside permease (cannot transport lactose into the cell.)They also found other mutants affected in lactose metabolism. lacl-mutants failed to regulate the lac operon.

Genes involved in metabolizing lactose

The lacl gene is upstream from the lac operon and encodes a repressor protein.The lacl gene product represses the expression of lacZ and lacY in the absence of lactose.

Negative control

When lactose is absent, the lacl repressor protein binds to the operator site and blocks transcription of the lac operon.When lactose is present, the lacl repressor protein does not bind to the operator site and transcription of lacZ and lacY is induced or "derepressed".The lac operon is said to be under negative control.

Relieving negative control

When lactose is present, lactose binds to the repressor, changing it conformation and releasing the repressor from the operator site.

What would be the characteristics of a lacl (loss of function) mutant?

B-galactosidase would be produced even in the absence of lactose.In the absence of a functional repressor (lacl mutant), the lac operon would be constitutively expressed (expressed in the absence of lactose)

To what element does the lac repressor bind in the absence of lactose?

lac operator

How does the lac repressor prevent the expression of the lacZ and lacY genes? By...

blocking transcription of the lac operon

Positive transcription control: the ara operon

The ara operon: -is under positive control by an activator protein-Is not transcribed when arabinose is not present-Is transcribed when arabinose is present.

The ara operon

This ara operon contains three genes required for arabinose metabolism, ara B, A, and D.Transcription of the ara operon is turned on by an activator protein called AraC encoded by the AraC gene.

The ara operon in the presence of arabinose

Arabinose positively regulates the ara operon.When Arabinose is present, the AraC protein binds to arabinose as a homodimer (two copies of the protein) and is allosterically regulated by arabinose.The arabinose-AraC homodimer binds to a regulatory sequence in DNA called the ara initiator. It lies just upstream of the promoter. Also binds to RNA polymerase.Interaction between AraC and RNA polymerase helps to dock the polymerase to the promoter and accelerate the initiation of transcription.AraC protein is both an activator in the presence of arabinose AND a repressor in the absence of arabinose.

ara operon in the absence of arabinose

When arabinose is absent, one monomer of the AraC dimer binds to the ara initiator. The other monomer binds to the ara operator.AraC protein bound to the ara operator works as a repressor that prevents transcription of both the ara operon and the araC gene.

Bacterial global gene regulation

Global gene regulation is the coordinated regulation of many genes, needed for responses that require the expression of dozens of even hundreds of genes.A regulon is a set of separate genes or operons that contain the same regulatory sequences and are controlled by a single type of regulatory protein.Regulons can be under negative control by a repressor protein OR positive control by an activator protein.

Regulons: Negative regulation example

Regulons allow bacteria to respond globally to challenges:-Shortages of nutrients-Sudden changes in temperature-Exposure to radiation-Shifts in habitat

Negative control

...

Post-translational control

...

...

...

Fiber composites (Chapter 11, Cell-Cell Interactions)

Like reinforced concrete, resist tension and compression. Concrete = the "ground" substance that resists compression-- (in cells, it is a gel-forming mixture of polysaccharides.)Steel rods = the "fibers" that resist tension.

Primary Cell Walls in Plants

The fibrous component consists of long strands of cellulose, which are bundled into stout, cable-like structures called "mictofibrils* and then cross-linked by other polysaccharide filaments. The microfibrils are synthesized by a complex of enzymes in the plasma membrane forming a criss-crossed network.The space between microfibrils is filled with gelatinous polysaccharides such as pectins-- the molecules that are used to thicken jams and jellies. Because the polysaccharides in pectin are hydrophillic, they attract and hold large amounts of water to keep the cell wall moist. The gelatinous components of the cell wall are synthesized in the rough ER and Golgi apparatus and secreted to the extracellular space.

Microfibrils

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Turgor pressure

The pressure inside of a cell as a cell (nucleus and cytoplasm) pushes itself against the cell wall. Because the concentration of solutes is higher inside the cell than outside, water tends to enter the cell via osmosis. This concept is especially important in young cells that are actively growing. Young plant cells secrete proteins called expansins into their cell wall. Expansins disrupt hydrogen bonds that corss-link the microfibrils in the wall, allowing them to slide past one another. Turgor pressure then forces the wall to elongate and expand. The result is cell growth.

Secondary Cell Walls in Plants

Between the plasma membrane and primary cell wall. The structure of the secondary cell wall varies from cell to cell in the plant and correlates with that cell's function. For example, cells on the surface of a leaf have secondary cell walls that are impregnated with waxes that form a waterproof coating. In cells that form wood, the secondary cell wall includes lignin, a complex polymer that forms an exceptionally rigid network.

The Extracellular Matrix in Animals (ECM)

Main function=structural support for cells. The ECM is a fiber composite that is secreted by animal cells. The ECM follows the same design as cell walls of bacteria, archaea, algae, fungi and plants. However, the animal ECM contains much more protein relative to carbohydrate than does a cell wall.The fibrous component of animal ECM is dominated by a cable-like protein called collagen. The matrix that surrounds collagen and other fibrous components contains gel-forming proteoglycans that consist of protein cores with many large polysaccharides attached to them.

Polysaccharides

A molecule formed by joining many monosaccharides together. Polysaccharides are typically energy-storage molecules (glycogen in animals, starch in plants) or structural molecules (cellulose in plants, chitin in exoskeletons).

exocytosis

a process by which the contents of a cell vacuole are released to the exterior through fusion of the vacuole membrane with the cell membrane.

How are ECM components synthesized, processed, and secreted?

Synthesized in the rough ERProcessed in the Gogli apparatusSecreted by exosytosis

integrins

membrane proteins that bind to extracellular proteins, including laminins, which in turn bind to other components of the ECM.

laminins

integrins can bind to laminins, which in turn bind to other components of the ECM.

middle lamella

connects adjacent plant cells. contains gelatinous polysaccharides, called pectins, that help glue together the walls of adjacent cells.

pectin

gelatinous polysaccharides

Check Your Understanding #1

Most cells secrete a layer of structural material that supports the cell and helps define its shape. The extracellular material is usually a fiber composite-- a combination of cross-linked filaments surrounded by a ground substance. You should be able to compare and contrast the molecular composition of a plant cell wall and the ECM of animal cells.

Compare and contrast the molecular composition of a plant cell wall and the ECM of animal cells

Plant cell walls and animal ECM's are both fiber composites. In plant cell walls the fiber component consists of cross-linked cellulose fibers, and the ground substance is pectin. In animal ECM's, the fiber component consists of collagen fibrils, and the ground substance is proteoglycan.

epithelium

a tissues that forms external and internal surfaces. Epithelial layers act as a barrier between the external and internal environments of plants and animals.

tight junction

a cell-cell attachment composed of specialized proteins in the plasma membranes or adjacent animal cells. Resembles quilting, where the proteins "stitch" the membranes of two cells together to form a watertight seal. Because of this, this junction is commonly found in cells that form a barrier, such as the epithelial cells lining the stomach and intestine. They are also dynamic, and can loosen to permit more transport and retighten. However, they are weak adhesions and require assistance from other sources as well.

desmosomes

Anchoring junctions that prevents cells subjected to mechanical stress from being pulled apart; button like thickenings of adjacent plasma membranes connected by fine protein filaments

selective adhesion

Cells adhere to other cells of the same tissue type

antibody

a protein produced by an immune response that binds specifically to a unique molecule type, often another protein. when an antibody binds to a protein, it can change the target protein's structure or interfere with its ability to interact with other molecules.

cadherins

the attachment molecules in desmosomes

gap junction

In animal cells, pores formed from connected membrane proteins that allow molecules to pass directly from cell to cell.

plasmodesmata

An open channel in the cell walls of plant cells allowing for connections between the cytoplasm of adjacent cells

symplast

In plants, the continuum of cytoplasm connected by plasmodesmata between cells.

apoplast

the network of cell walls and intercellular spaces within a plant body that permits extensive extracellular movement of water within a plant

signal receptor

protein that changes shape and activity after binding to a signaling molecule

signal transduction

conversion of a signal from one form to another. a long and often complex series of events ensues, collectively called a signal transduction pathway.

How cells can react to exchange of information

1. regulating gene expression2. activate or deactivate particular proteins

gap junctions

hydrophilic pores that allow the direct passage of ions and particles between two adjacent cells

plasmodesmata

An open channel in the cell walls of plant cells allowing for connections between the cytoplasm of adjacent cells, comparable to gap junctions in animal cells.Symplast: plasma membrane, insideApoplast: outside of the plasma membrane. consists of cell walls, middle lamella, and air spaces.

signal receptor

Any cellular protein that binds to a particular signaling molecule (e.g., a hormone or neurotransmitter) and triggers a response by the cell. Receptors for water-soluble signals are transmembrane proteins in the plasma membrane; those for many lipid-soluble signals (e.g., steroid hormones) are located inside the cell. Changes shape and activity after binding to a signaling molecule. (Like an "on" switch)

signal transduction

A series of molecular changes that converts a signal on a target cell's surface to a specific response inside the cell.

signal amplification

The process by which the binding of a single signaling molecule triggers progressively larger-scale responses along the signal transduction pathway.

G proteins

A class of proteins that reside next to the intracellular portion of a receptor and that are activated when the receptor binds an appropriate ligand on the extracellular surface.

second messenger

A small, nonprotein, water-soluble molecule or ion, such as calcium ion or cyclic AMP, that relays a signal to a cell's interior in response to a signal received by a signal receptor protein.

protein kinases

enzymes that activate or inactivate other proteins by adding a phosphate group to them

receptor tyrosine kinases (RTKs)

A receptor with enzymatic activity that can trigger more than one signal transduction pathway at once, helping the cell regulate and coordinate many aspects of cell growth and reproduction.

G-protein coupled receptors vs. enzyme-linked receptors

G-protein coupled receptors result in the production of second messengers, while enzyme-linked receptors drive phosphorylation cascades.

phosphatases

enzymes that remove phosphate groups-- always present in the cell and can deactivate signals in phosphorylation cascades.

crosstalk

signals from different pathways interact to modify the cell response

pheremones

chiemcial signals from one animal to another

quorum sensing

The ability of bacteria to sense the presence of other bacteria via secreted chemical signals.

stem cells

Cells that divide and remain undifferentiated, event through maturation. Three types are totipotent, pluripotent, and multi-potent.

cell proliferation

cells divide by mitosis and cytokinesis. The timing, location, and amount of cell division are regulated.

Cell-cell interactions

signals that are produced by cells influence their neighbors to divide, die, move, or differentiate.

Cell differentiation

undifferentiated cells specialize at specific times and places in a stepwise fashion

Cell movement and expansion

Cells can move past one another within a block of animal cells, causing drastic shape changes in the embryo.Cells can break away from a block of animal cells and migrate to new locations.Plant cells can regulate the plane of cell division and expand in specific directions, causing dramatic changes in shape.

Programmed cell death

The timing, location, and amount of cell death are regulated.

stem cell division

produces 2 daughter cells, only one stays a stem cell. this regulates stem cell population.

meristems

clusters of cells responsible for producing new cells at the ends of plants. responsible for the stems, roots, leaves, flowers, and other structures that develop throughout a plants life.

de-differentiation

adding as few as three transcription factors to adult cells can cause them to de-differentiate into cells that resemble those of the early embryo.

gastrulation

In animal development, a series of cell and tissue movements in which the blastula-stage embryo folds inward, producing a three-layered embryo, the gastrula.

germ cells

cells that produce sperm of eggs

apoptosis

Programmed cell death-- regulated by 2 genes. can cause neurological deficits if not maintained properly

genetic equivalence

all cells share same genes, they just express different ones.

differential gene expression

the expression of different genes by cells with the same genome; differences between cell types are not due to different genes, but due to differential gene expression

what is the most important process in controlling gene expression?

transcriptional control

regulatory transcription factors

General term for proteins that bind to DNA regulatory sequences (eukaryotic enhancers, silencers, and promotor-proximal elements), but not to the promotor itself, leading to an increase or decrease in transcription of specific genes.

pattern formation

events that determine the spatial organization of an embryo

morphogen

physical process that gives an organism its shape; Determines the body axes of the organism very early on.present in a gradient. cells can learn where they are along an axis by "reading" the concentration of a morphogen. (ex. bicoid)

bicoid gene

aids in anterior development; is a regulatory transcription factor (binds to DNA and activates genes required for the formation of exterior structures)

auxin

a plant hormone that promotes root formation and bud growth

segmentation genes

1. Morphogens (such as bicoid) control the formation of large groups of segments that span the anterior or posterior halves of the embryo.2. Gap genes are located along the head-to-tail axis and control the formation of groups of segments that define large body regions.3. Pair rule genes are expressed in alternating bands along the embryo, aid in the formation of individual segments4. Segment polarity genes expressed in a restricted band within every segment. Create specific regions within each segment.

Hox genes

Class of homeotic genes. Changes in these genes can have a profound impact on morphology. Hox genes play a key role in specifying which body structures to build.Don't know where "home" isVirtually all animals were found to possess related sets of Hox genes.

Regulatory gene cascade

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tool-kit genes

code for signals, signal transduction pathways, and regulatory proteins that are used to direct related aspects of development in many different species.

Hoxc6 and Hoxc8

expressed together in cells where ribs form, but Hoxc6 is expressed alone in the region that gives rise to the forelimbs

gastrulation tissues

ectoderm, mesoderm, and endoderm

ectoderm

One of the three primary (embryonic) germ layers formed during gastrulation. Ectoderm ultimately forms external structures such as the skin, hair, nails, and inner linings of the mouth and anus, as well as the entire nervous system.

mesoderm

middle germ layer; develops into muscles, bone, and much of the circulatory, reproductive, and excretory systems

endoderm

innermost germ layer; develops into the linings of the digestive tract and much of the respiratory system

blastocoel

the fluid-filled cavity inside a blastula

blastopore

The opening of the archenteron in the gastrula that develops into the mouth in protostomes and the anus in deuterostomes

organogenesis

process of organ formation that takes place during the first two months of prenatal development

somites

paired blocks of mesodermal tissue that extend along either side of the dorsal midline (top middle) of the embryo. stepping stone to the formation of muscle, lower (Dermal) layer of skin, and to much of the skeleton.

notochord

long supporting rod that runs through a chordate's body just below the nerve cord, in humans is transient, and only appears in the embryo. undergoes apoptosis.The notochord produces signaling molecules that induce the ectoderm on the dorsal (back) side of the embryo to fold. The notochord is a key organizing element during organogenesis.

neural tube

A tube of cells running along the dorsal axis of the body, just dorsal to the notochord. It will give rise to the central nervous system.The notochord produces signaling molecules that induce the ectoderm on the dorsal (back) side of the embryo to fold. The notochord is a key organizing element during organogenesis.

determination

the irreversible commitment of a cell to a particular developmental fate

myoblast

derived from cells in the somite; destined to become muscle cells but have not yet begun producing muscle-specific proteins.

gametogenesis

gamete formation

embryogenesis

in flowering plants, embryogenesis ends with the maturation of an ovule into a seed-- a structure that contains the embryo and a supply of nutrients surrounded by a protective maternally-provided coat.

germination

resumes growth to form a seedling when conditions are favorable. the beginning process of organogenesis.

vegetative development

produces the non-reproductive portions of the plant body--the roots, stems, and leaves.

reproductive development

there is no determined "germ line". a small group of cells in each stem have the potential to switch from vegetative to reproductive development in response to environmental conditions.

apical-basal cell

Basal cell= large bottom portion. Gives rise to the suspensor, which connects the embryo to surrounding tissues within the seed.Apical cell= top portion, gives rise to most of the embryo.only one cell of the basal portion gives rise to part of the embryo.

apical-basal axis

0

globular stage

radial axis is determined in the globular stage (interior of the plant body to the exterior)

cotyledons

embryonic leaves

hypocotyl

0

shoot

cotyledons and hypocotyl make up the shoot, which will become the above-ground portion of the body.

shoot apical meristem (SAM)

dome-shaped mass of dividing cells at the shoot tip

root apical meristem

Located just behind root cap. Responsible for growth of roots

3 plant embryonic tissues produced along the radial axis

1. epidermis: outer covering of specialized cells that protects the individual2. ground tissue: epidermal layer of cells, mass of cells that may later differentiate into cells that are specialized for photosynthesis =, food storage, or other functions3. vascular tissue: center of plant, will eventually differentiate into specialized cells that transport food and water between the root and shoot

MONOPTEROS

A gene that encodes a regulatory transcription factor that regulates the activity of target genes. Activated in response to signals from auxin-- a cell-cell signaling molecule. Auxin is produced in the shoot apical meristem and transported toward the basal parts of the individual. This results in an auxin concentration gradient along the apical-basal axis of a plant.

types of leaves leaves

0

determination in plants

doesn't occur or is readily reversible

the ABC model

What is the model called that proposes the products of 3 genes pattern the flower; each gene being expressed in two adjacent whorls?

MADS box genes

SIMILAR TO HOX GENES IN ANIMALSGenes that code for transcription factors that trigger the development of structures of each segment in a flowering plant

Dalton's Law

At constant volume and temperature, the total pressure exerted by a mixture of gases is equal to the sum of the partial pressures of the component gases

Flick's law of diffusion

1 is large,P2-P1 is large,and D is small

operculum

A protective flap that covers the gills of fishes. Creates a pressure gradient that moves water over the gills

ram ventilation

Method of forcing water over gills by swimming with mouth open

gill filaments

0

gill lamellae

0

cooperative binding

each successive oxygen bound to hemoglobin increases the affinity of the other subunits, while each successive oxygen released decreases the affinity of the other subunits

Bohr shift

A lowering of the affinity of hemoglobin for oxygen, caused by a drop in pH; facilitates the release of oxygen from hemoglobin in the vicinity of active tissues.

carbonic anhydrase

enzyme, large amount found in RBCs 1. the protons produced by the enzyme-catalyzed reaction induce the Bohr shift, which makes hemoglobin more likely to release oxygen2. The partial pressure of CO2 in the blood drops when carbon dioxide is converted into soluble bicarbonate ions, maintaining a strong partial pressure gradient favoring the entry of CO2 into RBCs

solute potential

the more solutes, the less free water concentration (lower water potential); solute potential= usually negativewater flows towards higher solute concentrations

water potential

The physical property predicting the direction in which water will flow, governed by solute concentration and applied pressure.

pressure potential

A component of water potential that consists of the physical pressure on a solution, which can be positive, zero, or negative.water flows away from areas of high pressure

evapotranspiration

Evaporation of water from soil plus transpiration from plants. Correlates with species richness.

root pressure

positive water pressure in roots, upward pushing, created osmotically

turgid plant

a plant's cytosol is full of water and the plasma membrane pushes against the cell wall

plasmolyzed cell

Plant cells that have lost so much water that turgor pressure is low

Concentrations of soil mineral ions are greater withinthe root than in the soil. How do root-hair cells do this?

active transport

active transport

Energy-requiring process that moves material across a cell membrane against a concentration difference

tension-cohesion theory

water movement to the top of tall trees is only possible because of the cohesive and adhesive properties of water