AP Bio

Conformational Change

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Explain how the location of enzymes in a cell influences metabolism

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Transport proteins involved in passive transport

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avtivators

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ion pump

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distinguish between kinetic and potential energy

A diver has more potential energy on the platform than in the water. Diving converts potential energy to kinetic energy, a diver has less potential energy in the water than on the platform. Climbing up converts the kinetic energy of muscle movement to potential energy once again.

Energy Coupling

A key feature in the way cells manage their energy resources to do this work is ______ the use of an exergonic process to drive an endergonic one. ATP is responsible for mediating most energy coupling in cells, and in most cases it acts as the immediate source of energy that powers cellular work.

Describe the relationship between free energy and equillibrium

A living cell is not in equillibrium so free energy allows the reactions to occur. The overall sequence of reactions is kept going by the huge free energy difference between glucose and oxygen for example.

cotransport

A single ATP powered pump that transports a specific solute can indirectly drive the active transport of several other solutes in a mechanism called ____

electrogenic pump

A transport protein that generates voltage across a membrane. The sodium potassium pump appears to be the major one of animal cells.

Describe the structure of ATP and explain in general terms how ATP performs cellular work

ATP contains the sugar ribose with the nitrogenous base adenine and a chain of three phosphate groups bonded to it. ATP is also one of the nucleoside triphosphates used to make RNA. The cell's proteins harness the energy released during ATP hydrolysis in several ways to perform three type of cellular work- chemical, transport and mechanical. page 149-152 When it hydrolisis, it gets ADP and Pi which gives off energy so basically: Energy from catabolism (exergonic, energy releasing processes) goes to hydrolysis, then energy for cellular work (endergonic energy-consuming processes) producess ADP and Pi

membrane potential

All cells have voltages across their plasma membranes. Voltage is electrical potential energy-a seperation of opposite charges. The cytoplasmic side of the membrane is negative in charge relative to the extracellular side because of an unequal distribution of anions and cations on the two sides. The voltageacross a membrane called _____ ranges from about -50 to -200 milivolts (mV) (The minus sign indicates that the inside of the cell is negative relative to the outside)

Lipid

Are not polymers. They also have little or no affinity for water, thus they mix poorly. They are hydrophobic and the structures are dominated by nonpolar covalent bonds.

Write and define each component of the equation for free energy change (delta G)

At equilibruim delta G = O (cell is dead) positive or zero the g are never spontaneous. The formula is delta G = delta H - T delta S Delta H symbolizes the change in the system's enthalpy (equivalent to total energy); delta S is the change in the system's entropy; and T is the absolute temperature in kelvin unitits. We can now see if it spontaneous by looking at G. Only processes with a negative G are spontaneous. For G to be negative either H must be negative (the system gives up enthalpy and H decreases) or T delta S must be positive (the system gives up order and S increases) or both: when H and TS are tallied, G has a negative value.

Transport proteins involved in active transport of ions and small molecules

Carrier proteins.

Describe the three main kinds of cellular work

Chemical work - the pushing of endergonic reactions that would not occur spontaneously, such as the synthesis of polymers from monomers. Transport work- the pumping of substances across membranes against the direction of spontaneous movement. Mechanical work- such as the beating of cilia, the contraction of muscle cells, and the movement of chromosomes during cellular respiration.

inhibitors

Competetive and non-combetitive. competetive binds to the active site. noncompetetive binds to a different site on the enzyme.

First law of thermodynamics

Energy of the universe is constant. Energy can be transferred or transformed, but cannot be created or destroyed.

Second law of therodynamics

Every energy transfer or transformation increases the entropy of the universe.

phagocytosis

IN ____ a cell engulds a particle by wrapping pseudopodia (singular pseudopodium) arounf it and packaging it within a membranous sac called a food vacoule. The particle will be digested after the food vacuole fuses with a lysosome containing hydrolytic enzymes. endocytosis cellular eating

pinocytosis

IN _____ the cell gulps droplets of extracellular fluid into tiny vesicles. It is not the fluid itself that is needed by the cell, but the molecules dissolved in the droplets. Because any and all included solutes are taken into the cell, this is nonspecific in the substances it transports. endocytosis cellular drinking

endocytosis

IN _____ the cell takes in biological molecules and particulate matter by forming new vesicles from the plasma membrane. Although the proteins involved in the processes are different, the events of this look like the reverse of exocytosis.

receptor-mediated endocytosis

IN____ enables the cell to acquire bulk quantities or specific substances, even though those substances may not be very concentrated in the extracellular fluid. Embedded in the membrane are proteins with specific receptor sites exposed to the extracellular fluid, to which specific substances (ligands) bind. The receptor proteins then cluster in regions of the membrane called coated pits, whic are lined on their cytoplasmic side by a fuzzy layer of coat proteins, Next each coated pit forms a vesicle containing ligand molecules. notice that there are relatively more bound molecules (purple) inside the vesicle, but other molecules (green) are also present. After the ingested material is liberated from the vesicle, the emptied receptors are recycled to the plasma membrane by the same vesicle. Very specific in what is transported! examples: cholesterol travels in the blood in low density lipoporteins. -familial hypercholesterolemia (inherited disease) Cell acquires specific materials from the environment.

Distinguish between exergonic and endergonic reactions in terms of free energy change (delta G)

If a chemical process is exergonic (downhill), releasing energy in one direction, then the reverse process must be endergonic (uphill) using energy.

Explain how substrate concentration affects the rate of an enzyme-catalyzed reation

If you add substrates, the reaction rate gets faster. Eventually it starts to level out and reaches a platue. If you are going to increase the reaction rate then what you need to do is double the amount of enzymes.

Describe several mechanisms by which enzymes lower activation energy

In an enzymatic reaction, the substrate binds to the active site of the enzyme. The active site can lower the activation energy barrier by: orienting substrates correctly, straining substrate bonds, providing a favorable micro environment, covalently bonding to the substrate

cooperativity

In another kind of allosteric activation, a substrate molecule binding to one active site in a multisubunit enzyme triggers a shape change in all the subunits, thereby increasing catalytic activity at the other active sites. called ______ this mechanism amplifies the respone of enzyme to substrates. This is considered allosteric regulation because binding of the substrate to one active site affects catalysis in another active site.

Identify an ester linkage and describe how it is formed

In making a fat, three fatty acid molecules are each joined by this linkage. A bond between a hydroxyl and carboxyl group. This results triclyglycerol.

Concentration Gradient

In the absence of other forces, a substance will diffuse from where it is more concentrated to where it is less concentrated. Any substance will diffuse down its _____, the region along which the density of a chemical substance increases or decreases. This is also spontaneous and decreases free energy and increases entropy.

Steroids

Include cholesterol and certain hormones. These are lipids with a carbon skeleton consisting of four fused carbon rings. Remember that different steroids have different functional groups attached to the rings.

Endergonic reaction

Is one that absorbs free energy from its surroundings. because this kind of reaction essentially stores free energy in molecules (G increases), delta G is positive. Such reactions are nonspontaneous, and the magnitude of delta G is the quantity of energy require to drive the reaction.

Describe the fluidity of components of a cell membrane

Lipid bilayer...phospholipid comes together no-covalently so they are weak. Membrane molecules are also mobile. Most lipids, some proteins can drift laterally in the membrane. Lateral movement occurs often, and flip flopping accross membrane is rare. (once a month)

Phospholipids

Major components of cell membrane. Cells cannot exist without it. They are essential for cells because they make up cell membranes. It is similar to a fat molecule but has only two fatty acids attached to glycerol rather than three. The third hydroxyl group of glycerol is joined to a phosphate group, which has a negative electrical charge in the cell. Lastly, small molecules, which are usually charged or polar, can be linked to the phosphate group to form a variety of phospholipids.

cofactors

Many enzymes require helpers for catalytic activity. These adjuncts are called ____ may be bound tightly to the enzyme as permanent residents or they may bind loosely and reversibly along with the substrate. organic ones- coenzymes

Explain the role of catabolic and anabolic pathways in cellular metabolism

Metabolism as a whole manages the material and energy resources of the cell. Some metabolic pathways release energy by breaking down complex molecules to simpler compounds. This is called _____. ____ pathways consume energy to build complicated molecules from simpler ones.

Explain why an investment of activation energy (EA) is necessary to initiate a spontaneous reaction

Molecules are stable. In order to be reactive, they must be unstable. Therefore, energy must be added to molecule in order for them to reach the transition state where their bonds can be broken. The bonds break only when the molecules have absorbed enough energy to be unstable.

Diffusion

Molecules have a type of energy called thermal energy (heat), due to their constant motion. One result of this motion is _____ the movement of molecules of any substance so that they spread of evenly into the available space. Movement of an individual molecule is random. Net movement of molecules from regions of high concentration to low concentration. Rate of diffusion depends on concentration gradient and molecular size.

Hydrophobic

Non- water loving

Explain why highly ordered living organisms do not violate the second law of thermodynamics

Order can increase locally (in organisms and cell), but net effect is randomization of the universe. Living organisms take in organized forms of matter and energy, and replace them with less ordered forms.

Fatty Acid

Part of what makes up fat. It has a long carbon skeleton. 16-18 carbon atoms in length. The carbon at one end of the skeleton is part of a carboxyl group. This is what gives it its name.

Describe the function of enzymes in biological systems

Protein catalysts. breaking down sucrose into glucose and fructose. Catalysts can be used over and over again. Enzymes speed reactions by lowering Activation Energy- Transistion state can be reached at cell temperature. Enzymes do not change delta G. The height of the barrier is lower. It increases the reaction rate.

Explain how enzyme structure determines enzyme specificity

Recall that most enzymes are proteins and proteins are macromolecules with unique three dimensional configurations. This shape is what it depends on. Which is a consequence of its amino acid sequence

Explain how cholesterol resists changes in membrane fluidity with temperature change

Reduces fluidity at warm temperatures. Restrain movement of phospholipids. Maintains fluidity at cool temperatures. prevents tight packing. Cells can modify composition and thus fluidity.

Thermodynamics

Study of energy transformations that occur in a collection of matter is called ___

Active Site

Substrate binds to this on the enzyme

exocytosis

The cell secretes certain biological molecules by the fusion of vesicles with the plasma membrane this process is ____ A transport vesicle that has budded from the golgi apparatus moves along microtubles of the cyctoskeleton to the plasma membrane. When the vesicle membrane and plasma membrane come into contact specific proteins rearrange the lipid molecules of the two bilayers so that the two membranes fuse. -lipid bilayer fuse and spill contents of vesicle to the outside -transport vesicles are moved to the plasma membrane

Passive transport

The diffusion of a substance across a biological membrane is _____ because the cell does not have to expend energy to make it happen.

feedback inhibition

The end product of a metabolic pathway allosterically inhibits the enzyme for a previous step in the pathway.

Activation Energy

The initial investment of energy for starting a reaction- the enrgy required to contort the reactant molecules so the bond can break is known as the free energy of activation or...

proton pump

The main electrogenic pump of plants, fungi and bacteria is ____ this actively transports protons (hydrogen ions H+) out of the cell. The pumping of H+ transfers positive charge from the cytoplasm to the extracellular solution

Explain how metabolic pathways are regulated

The metabolic pathways are regulated by processes called induction and repression. This basically uses whatever is naturally found in the environment to the advantage of the organism. For example, if lactose is not present in the environment, then the bacteria that typically use it will induct another substance and repress their need of lactose.

Explain how temperature, PH, cofactors, and enzyme inhibitors can affect enzyme activity

The rate of an enzyme reaction increases with increasing temperature up to a point. After that point, the rate of the reaction will drop. The same thing occurs with pH. The cofactors can be bound tightly or loosely to the enzyme. Coenzymes act as organic helpers and perform a crucial function in catalysis. Competitive inhibitors mimic the substrate. Noncompetitive inhibitors bind to another part of the enzyme altering its shape.

Peripheral Proteins

These are not embedded in the lipid lilater at all; they are appendages loosely bound to the surface of the membrane, often to exposed parts of integral proteins.

Adenosine triphosphate (ATP)

This contains the sugar ribose, with the nitrogenous base adenine and a chain of three phosphate groups bonded to it. In addition to its role in energy coupling, it is also one of the nucleoside triphosphates used to make RNA

sodium-potassium pump

This exchanges NA for K across the plasma membrane of animal cells. The function of your brain is dependent on these pumps, your muscles too! Extra cellular has high NA+ and low K+ and intrecellular has low NA+ and high K+

Cholesterol

This is a crucial molecule in animals. It is a common component of animal cell membranes and is also the precursor from which other steroids are synthesized. In vertebrates, cholesterol is synthesized in the liver and obtained from the diet. A high level of this may contribute to atherosclerosis.

Fluid Mossaic model of membrane structure

This is how phospohlipids and proteins arranged in the membranes of cells. The membrane is a fluid structure with a mosaic of various proteins embedded in or attached to a double layer (bilayer) of phospholipids.

Ester Linkage

This is the bond between hydroxyl and carboxyl groups that hold together fat.

vesicle

This is where large molecules cross the plasma membrane and it is packaged in it

Saturated Fatty Acid

This type of fatty acid has no double bonds C-C. There is a hydrogen at every possible position. It is a straight chain. It is also solid at room temperature and can lead to cardiovascular disease.

Unsaturated Fatty Acid

This type of fatty acid has one or more double bonds C-C. It is formed by removal of H atoms from the carbon skeleton. It is also kinked in structure (CIS) at the double bond. Liquid at room temperature and better for cardiovascular health.

Active membrane transport

To pump a solute across a membrane against its gradient requires work; the cell must expend energy. These are all carrier proteins not channel proteins.

electronchemical gradient

Two forces drive the diffusion of ions across a membrane: a chemical force (the ion's concentration gradient- chemical force diffusion from high to low concentration) and an electrical force (the effect of the membrane potential on the ion's movement towards opposite polarity.) This combination of forces acting on an ion is called _______ -The driving force for passive transport of ions across cell membrane. -Na and K are important for electrically excitable cell function (for nerves and muscles) -H is important for metabolism

Enzyme

a catalytic protein. a macromolecule that acts as a catalyst Biological catalysts

Entropy

a measure of disorder or randomness. The more randomly arranged a collection of matter is, the greater its entropy. Most of entropy takes the form of increasing heat.

Metabolic pathways

alterations of molecules in steps.

Metabolism

an emergent property of life that arises from orderly interactions between molecules. All of an organisms's chemical reactions.

Why are phospholipids amphipathic molecules

both (hydrophobic and hydrophillic) characters in it.

Catabolic pathways

breakdown of complex molecules (release energy) Example is cellular respiration

Anabolic pathways

build complex molecules (consume energy, energy released by catabolic pathways drives this pathway) *proteins for example*

Explain the role of membrane carboyhrdrates in cell-cell recognition

cells can distinguish one type of neighboring cell from another. Important for organization of cells as tissues and organs during development. Important for rejection of fereign cells (immune system) molecules in membrane are also modified with carbohydrates.

Catalyst

changes reaction rate without being consumed (changed) A chemical agent that speeds up a reaction without being consumed by the reaction.

Describe the properties of phospoholipids and their arrangement in cellular membranes

contains a glycerol backbone. It also contains 2 fatty acids. There is a phosphate group at the 3rd position of glycerol. (negative charged) Hydrocarbon chain of fatty acid is hydrophobic, charges make phosphate group hydrophilic.

Glycolipids

covalently bonded to lipids. This forms this molecule.

Glycoproteins

covalently bonded to proteins. This forms.

Osmosis

diffusion of water across a selectively permeable membrane. (special case of passive transport)

The building block molecules

fats phospholipids and steroids

Name the principal energy storage molecules of plants and animals

fats. it stores in the reserves in adipose cells (the yellow fat you find on chicken)

Hypertonic

higher solute concentration H2O molecules move through selectively permeable membrane from hypotonic solution to hypertonic solution Animal cell shriveled plant cell plasmolyzed

Chemical Energy

is a term used by biologists to refer to the potential energy available for release in a chemical reaction. (example: food)

Fat

large molecules assembled from glycerol and fatty acids by dehydration reactions. Glycerol is an alcohol; each of its three carbons bears a hydroxyl group.

bulk transport

large molecules. Exocytosis and Endocytosis.

Hypotonic

lower solute concentration H2O molecules move through selectively permeable membrane from hypotonic solution to hypertonic solution Animal cell lysed (breaks) plant cell turgid (normal)

Facilitated diffusion including channel proteins

many polar molecules and ions impeded by the lipid bilayer of the membrane diffuse passively with the help of transport proteins that span the membrane. This is called. TWO types of transport proteins are channel proteins and carrier proteins. Channel proteins simply provide corridors that allow specific molecules or ions to cross the membrane.

Selective permeability

membranes allow some substances to cross more easily than others.

expalin how membrane fluidity is influenced by temperature and membrane composition

membranes with unsaturated fatty acids are more fluid. Kinks in tails prevent tight packing. Temperature- membranes switch from fluid state to solid state at cool temperatures.

Integral (transmembrane) proteins

penetrate the hydrophobic interior of the lipid bilayer. The majority are transmembrane proteins which span the membrane; others extend only partway into the hydrophobic interior.

Selective Permeability (lipid bilayer and membrane proteins componenets)

phospholipid bilayer component of a biological membrane's ____ Gases- (CO2, N2, O2) because they are small they can slip very easily. Small unchargerd (polar molecules) - Ethanol can pass through easily, but H20 and other can pass but it does have a harder time. The larger uncharged polar molecules such as Glucose. It can not move between. It does not move across the membrane. , Ions and charged polar molecules can also NOT pass through. So the only ones that can easilly pass through is Gases and small uncharged (some)

Free Energy change (delta G)

portion of a system's energy that is able to perform work. (constant T)

Exergonic reaction

proceeds with a net release of free energy. Because the chemical mixture loses free energy (G decreases), delta G is negative for an exergonic reaction. Using delta G as a standard for spontaniety, exergonic reactions are those that occur spontaneously (energetically favorable) The greater the decrease in free energy, the greater the amount of work that can be done. Use cellular respiration as an example.

Substrate

reactant that binds to an enzyme.

Cell Membrane (plasma membrane)

seperates the living cell from its nonliving surroundings

Isotonic

solutions with equal solute concentrations Osmosis continues until solutions are isotonic Normal in animal Flaccid in plant

Product

substrate converted to products (may be reversible)

Free Energy

the portion of a system's energy that can perform work when temperature and pressure are uniform throughout the system, as in a living cell. Initial state- higher energy (diver on board), final state-more stable (diver jumping off)

Amphipathic molecule

these are considered to be both hydrophobic and hydrophilic (phospholipid component)

Explain why an organism is considered an open system

they cannot survive without continuously exchanging matter and energy with their environment. The peculiarity of open systems is that they interact with other systems outside of themselves. This interaction has two components: input, that what enters the system from the outside, and output, that what leaves the system for the environment.

lipid bilayer

this is the arrangement of membrane phospholipids. Note that it is hydrophobic tails from core and hydrophillic heads on outside. There is a barrier between cell and external environment and a barrier between cell and internal organelles.

Triacylglycerol

three fatty acids joined to glycerol by ester linkages. These three fatty acids can be the same or different. The nonpolar C-H bonds in the long hydrocarbon skeleton make fats hydrophobic.

allosteric regulation

use to describe any case in which a protein's function at one site is affected by the binding of a refulatory molecule to a separate site. It may result in either inhibition or stimulation of an enzyme's activity.