Biology 225 test 2

What is the fluidity of a lipid bilayer

the ease molecules move through the lipid bilayer is important for membrane function and has to be maintained within certain limit. How fluid a lipid bilayer is at a given temperature depends on its phospholipid composition and nature of hydrocarbon tails. The closer and more packed the tails, the less fluid the bilayer will be. The length and number of double bonds (saturated and unsaturated) affects how the tails will tightly pack. Shorter chain length reduces the tendency of the hydrocarbon tails to interact with one another and increases the fluidity of the bilayer.

Protein phosphorylation involves

the enzyme-catalyzed transfer of the terminal phosphate group of ATP to the hydroxyl group on a serine, threonine, or tyrosine side chain of the protein. Protein phosphorylation is catalyzed by protein kinase. the removal of the phosphate group is catalyzed by a protein phosphatase

resonance stabilization of both products of hydrolysis

the phosphate group ion is resonance-stabilized because the extra electron pair formally shown as part of a P=O double bond is delocalized over all four O atoms adjacent to the central P [instead of being delocalized over only three O atoms, as occurs when the phosphate group is bound to ATP].

What is equilibrium

the rates of the forward and reserve reactions are equal, and there in no further net change in the concentrations of substrate or product. (the concentration of the substrate is equal to the concentration of product). Free energy change = zero and the reaction will not proceed forward or backward, and no work can be done.

What is competitive inhibition

the substrate and non-substrate molecules (Competitive inhibitors) are competing for the active site. 1. Is sensitive to the relative concentration of substrate and not real substrates (competitive inhibitors).

Although order of amino acids give the proteins their shape and function

they are not enough by themselves to determine the protein shape and function. Proteins use non-protein molecules to perform functions that would be difficult or impossible using amino acids alone. EX: non-protein Hemoglobin--carries four non-covalently heme-group (prosthetic group) Heme-group give hemoglobin (and blood) its red color and allow hemoglobin to pick up oxygen in the lungs and release it in the tissues. When hemoglobin and other small molecules (non-proteins) are attached covalently and permanently to the protein they become an integral part of the protein molecule itself.

Enzymes can bind more than one substrate if

they are structurally similar. EXample: Beta-galactosidase hydrolyzes the glycosidic bond when the galactose portion of the substrate molecule is in its active site.

• Hydrophilic molecules dissolve in water

they contain charged atoms or polar groups that have uneven distribution of positive and negative charges. The atoms can form electrostatic forms (ionic bonds) and hydrogen bonds with polar water molecules.

Anabolic pathways (anabolism)=

use the energy produce by catabolism to drive the synthesis of many molecules that form the cell. (done in Rough ER)

Many of the drugs

we take to treat or prevent illness work by blocking a particular activity of an enzyme

• Lipids form lipid bilayers in water

whenever there is an amphipathic molecule. The hydrophilic molecule dissolves and loves water. The hydrophilic head is attracted to water but the hydrophobic tails do not. They shun water and aggregate with other hydrophobic molecules. Once the hydrophobic molecules shun away from water, they form lipid bilayers to separate themselves from water. As a result, the hydrophilic heads face the water from both surfaces of the bilayer sheets. The hydrophobic tails are shielded from the water as the lie next to one another in the interior like a sandwich. • The bilayer seal themselves when there is a tearing that allow water to enter through the hydrophobic environment. It is cannot reseal itself, it create close vesicles.

how the enzyme performance is measured?

• An enzyme's performance depends on how rapidly it can process its substrate. The rate of an enzyme reaction increases until a maximum value (Vmax) is reached. At this point all substrate-binding sites on the enzyme molecules are fully occupied, and the rate of reaction is limited by the ratio of the catalytic process on the enzyme surface. For most enzymes the concentration of substrates at which the reaction is half-maximal (KM) is direct bound with a large value of KM (a large amount of substrate needed) corresponding to weak binding.

How enzymes lower the activation energy

• At higher temperature, enzymes push reactants (substrate) over the activation energy barrier to convert them into products. • Each enzyme bind to one or two substrates • It holds the substrates in a way that greatly reduces the activation energy needed to facilitate a specific reaction to occur between the molecules. • Catalyst is a substrate that can lower the activation energy to speed up the reaction. • Catalyst increase the rate of chemical reactions because they allow a much larger proportion of the random collisions with surrounding molecules to kick the substrates (reactant) over the energy barrier Through diffusion, enzymes and substrates find each other because motions are fast at molecular level. Because of heat molecules are in constant morion and take the space inside the cell very effientyl randomly. In this way every olecule in a cell collides with a huge number of other molecules each second How enzymes hold substrates in order to lower the activation energy? 1. Enzyme binds to two substrate molecules to orient them in a way that a reaction will occur between them. 2. Binding of substrates to enzymes rearranges electrons on the substrate creating partial negative and partial positive charges that favor the reaction 3. Enzymes strains the bound substrates molecule, forcing it toward a transition state that favor a reaction

amphipathic

• Molecules with hydrophobic and hydrophilic head are called amphipathic which is found in sterols such as cholesterol found in animal cell membrane and glycolipids= have sugars has part of their hydrophilic head.

What is the difference between living being and nonliving beings

• Nonliving things such as buildings crumble and dead organisms decay left to themselves become disordered. • Living cells maintain and generate order at every level for example a butterfly or flower to the organizations of molecules that make up them. Living cells generate order by using cellular mechanisms that extract energy from the environment and convert it into energy stored in chemical bonds. (Living organisms are the same even if they are changed or recycles. Ex: my body is the same today as it was 10 years ago even though I have new atoms that did not exist 10 years)

The paper example

• Paper burns easily, releasing into atmosphere water and carbon dioxide as gases and energy as heat. Paper + oxygen= smoke+ ashes+ heat+ carbon dioxide+ water 1. This reaction is only one way because smoke and ashes never spontaneously gather carbon dioxide and water from the heated atmosphere and reconstitute themselves into paper. The paper chemical energy is converted into heat and not get loss because energy cannot be created or destroyed; but is dispersed in the chaotic and randomness of the universe= heat= chaotic random thermal motions of the molecules. At the same time, the atoms and molecules of the paper become dispersed and disordered. This means there was a release in free-energy (bonds have been broken, energy was required to break bonds. An exergonic reaction. Spontaneous reaction Chemical reactions go only in the direction that leads to a loss of free energy which is the spontaneous direction. The spontaneous direction for any reaction is the direction that goes downhill because is energetically favored and is decreased. • A paper or living organisms cannot spontaneous burst into flame or disappear because the molecules in the paper and living organisms are stable (have lower energy to initial the reaction). They need a boost over an energy barrier before it can undergo a chemical reaction that moves it to a lower-energy (or more stable). The boost is called activation energy

Explain how Y is converted to X

• Reactant (Y) is relatively in stable state (lower-energy). Energy is required to convert reactant to product (X) • Product (X) is even at lower energy level than reactant. • The conversion of Y to X will not take place if Y does not acquire enough activation energy from its surroundings (energy a and energy •Forward reactions: Activation energy= a-b • Reserve reaction (X to Y) requires even more activation energy and occurs rarely because it requires more activation energy. Activation= a-c. Total energy change= free energy change for spontaneous reaction = c-b which is negative number. • The activation energy for a specific reaction can be lowered by catalysts (d). . • Enzymes reduce the activation energy for the reaction they catalyze to allow chemical reaction to occur. In the case of paper the activation energy is provided by the heat of the lighted match. For the molecules in the watery solution inside a cell, the boost is delivered by energetic random collision with surrounding molecules—collisions that become more violent as the temperature is raised.

The Lipid Bilayer is Asymmetrical

• The cell membrane are generally asymmetrical: • Phospholipids and glycolipids are asymmetrically distributed in the plasma membrane. They present a very different face for the interior of the cell or organelles than they show ti the exterior. Phospholipids are made in endoplasmic reticulum. Flippases play a role in synthesizing the lipid bilayer. Newly synthesized phospholipid molecules are all added to the cytosolic side of the ER membrane. Flippases then transfer some of these molecules to the opposite monolayer, so that the entire bilayer expands

is saturated

• The fatty acid without double bond and with maximum number of hydrogen bonds is saturated and cannot break easily at higher temperature. • EX: Butter is saturated at room temperature because it double bonds have been removed and have additional hydrogen bonds.

How membrane lipids form bilayers in water?

• The type of lipids in cell membrane is phospholipid, Cholesterol and glycolipid. But the Phospholipid is the most common. • The major type of molecule present in a cell membrane is a phospholipid. It has a hydrophilic head region, which is composed of a polar group attached to a phosphate group. The phosphate group is attached to a glycerol, which is attached to two fatty acid tails. The glycerol and fatty acid tails comprise the hydrophobic region of the membrane. • The most common type of phospholipid in cell membrane is phosphatidylcholine • Phosphatidylcholine has the small molecule chlorine attached to a phosphate as its hydrophilic head and two long hydrocarbon chains as its hydrophobic tails

Plasma membrane

Is the only membrane in prokaryotic and eukaryotic bacteria. It is involved in cell communication, import and export of molecules and cell growth and motility. o Ex: Receptor Proteins in the plasma membrane enable the cell to receive signals from the environment. o Transport proteins in the plasma membrane enable the import and export of small molecules o Flexibility of the membrane and its capacity for expansion allow cell growth and cell movement. When a cell grows or changes shape, the membrane takes the shape of the cell by adding new membrane (eukaryotic cells) continuously and can deform without ever tearing. o Prokaryotic cells only have a single membrane. Eukaryotic cells have internal membranes that encloses organelles such as ER, Golgi Apparatus, mitochondria etc . The internal and external organelles have the same function and structure as the plasma membrane

Why Cells exist in a state of chemical disequilibrium

Living cells avoid reaching a state of equilibrium because they are constantly exchanging materials with their environment: taking in nutrients and eliminating waste products. Reactions in cells are not in equilibrium because the products of one reaction are siphoned off to become the substrates in the next reaction. Rarely products and substrates reach concentrations at which the forward and reserve reactions rates are equal.

Effect of substrates concentration on enzyme activity

To catalyze a reaction an enzyme must bind first to it substrate The substrate undergoes a reaction to form a product and remain connected to the enzyme. The product is released and diffuses and leave the enzyme free to bind another substrate molecule and catalyze another reaction If the concentration of the substrate is increased progressively from a very low value, the concentration of the enzyme-substrate complex and the rate at which products form increases in linear line As more and more enzymes molecules become occupied by substrate. When it is occupied by a higher concentration of substrates, it reaches the maximum value, (Vmax)) Vmax indicate that the active sites of all enzyme molecules in the sample are fully occupied by substrates and the rate of product formation depends only on how rapidly the substrate molecules can be processed. Turnover number is around order of 1000 substrates molecules per second. Enzyme can form around 1000 substrates molecules per second.

In contrast to the hydrophobic side chains

, the peptide bonds that join the successive amino acids in a protein are normally polar, making the polypeptide backbone hydrophilic The backbone form a hydrogen bonds with one another H-bond is maximized if the polypeptide chain forms a regular alpha helix, and this make the membrane-spanning segments of polypeptide chains to traverse the bilayer as alpha helix. The membrane-spanning alpha helices--the hydrophobic side chains are exposed on the outside of the helix, where they are in contact with the hydrophobic lipid tails and atoms in the polypeptide backbone form hydrogen bonds with one another on the inside of the helix. In trans-membrane proteins, the polypeptide chain crosses the membrane only once. Other trans membrane proteins form aqueous pores that allow water-soluble molecules to cross the membrane (this requires a lot of alpha helices)

Feedback inhibition at multiple sites regulates connected metabolic reactions

. Feedback inhibition regulates amino acid synthesis

Be able to explain how membrane is generated in a eukaryotic cell

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Be able to explain the fluid mosaic model of cell membrane structures and why fluid mosaic is an appropriate description of a cell membrane

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Be able to explain why membrane fluidity is important and the various factors that can affect membrane fluidity

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Be able to identify types of molecules that compose a cell membrane and describe in detail a membrane's overall organization

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Explain why integral proteins include one or more aloha helices are part of cell membrane components?

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How A Polypeptide Chain Usually Cross the Bilayer as Alpha Helix?

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How Fatty acid tail saturation affects fluidity

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How cholesterol affects the fluidity of cell membrane

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How is orientation of a plasma membrane maintained during the fusion of budding of vesicles

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The Fluidity of a Lipid Bilayer Depends on its Composition

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What do membrane Protein do?

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explain why membrane fluidity is important

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Membrane fluidity is important because

1. Allow membrane proteins (transporter and ion channels) to diffuse rapidly in the plane of the bilayer and interact with one another 2. Allow membrane to diffuse with one another and mix their molecules 3. Make sure that membrane molecules are distributed evenly between daughter cells when a cell divides 4. It allows cell to live, grow, and reproduce. Without fluidity, all this could not happen

Identify key factors that affect enzyme kinetics and then explain how and why enzyme kinetics are affected by these factors?

1. Amount of enzyme and substrates 2. Enviornmental factors (ph, salt, and T) 3. Inhibitors

Substrate concentration

1. At lower substrate concentration the enzyme will not easily find the substrate and the rate of reaction will decrease/ activation energy increase. 2. Increasing substrate concentration, helps enzymes to find the substrates easily and the rate of reaction increase in a linear fashion.

Enzymes have an optimal temperature for activity Increasing temperature (normal optimal)

1. Causes the molecules to vibrate and rotate more. 2. Enzyme molecules vibrate faster and active site changes shape faster 3. As the molecules vibrate,the active site changes shape. This determines the rate at which it catalyzes the reaction 4. Enzyme and substrates stick together faster to form enzyme substrate-complex because they are moving around more 5. More substrates molecules have sufficient energy to start the reaction because heat is added.

How can phosphorylation control protein activity by triggering a conformational change

1. Covalent modification by phosphate group to regulate enzyme activity. Enzyme are regulated by attaching a phosphate group covalently to one of its amino acids site chains. EX: enzyme that catalyzed addition of a phosphate group to a protein cause a major conformation change by attracting a cluster of positively charged amino acid site chains. This can affect the binding of ligand else where an the surface of protein. Removal of phosphate group by a second enzyme returns the proteins to its original conformation and restores its initial activity. This protein phosphorylation controls the activity of many different types of proteins in eukaryotic cells.

What enzymes do not do?

1. Do not speed unfavorable reactions/non-spontaneous (do not speed up reactions in anabolic pathways without coupling them with an energetically favorable reaction)

Decreasing temperature (bellow the optimal temperature)

1. Enzyme molecules vibrate less and active sites change slowly. 2.Substrates go in the active site less frequently 3. Few substrates molecules have enough energy to react

Enzymes can encourage catalysis in several ways

1. Hold substrates together in a precise alignment (enzyme binds to two substrates molecules and orients them precisely to encourage a reaction between them 2. Charge stabilization of reaction intermediates (binding of substrate to enzyme rearranges electrons in the substrate, creating partial negative and positive charges that favor a reaction 3. Altering bond angles in the substrate to increase the rate of a particular reaction ( enzyme strains the bound substrate molecule, forcing it toward a transition state to favor a reaction

Determining how an inhibitor decreases and enzyme activity

1. How a metabolic pathway is regulated 2. Suggest how those control point can be circumvented by carefully designed mutation in specific genes

Questions:

1. How cells obtain energy from the environment to create the order 2. Why a constant input of energy is needed to sustain living organisms? 3. How enzymes catalyze the reactions that produce biological order? 4. Describe the molecules that carry the energy that makes life possible

The amount of substrates influence

1. How well or how quicly an enzyme works. 2. Enzymes can also be controlled by products, substrate lookalikes, inhibitors, toxins, and other small molecules that either increase or decrease their activity

How enzymes convert reactants to product? How enzymes catalyze the reactions that produce biological order?

1. In order for enzymes to catalyze a reaction must form a complex with a reactant, or substrate. 2. The enzyme and substrate meet and stick together at the active site to form an enzyme-substrate complex. 3. The substrates only fit in the active site of the enzyme (like lock and key). The active site is a fold or pocket. 4. The enzyme-substrate complex catalyze the reaction and form a product. 5. The product is released in the environment because it does not fit in the active site. 6. Then, the enzyme is ready to form a complex with another substrates and is not used in reactions. 7. This same enzyme can be used over and over again. (similar substrates can bind to this enzyme to form enzyme substrate complex)

Some examples of Co-enzymes and their vitamin source

1. NAD+ get vitamin from nicotinic acid (niacin or vitamin B5) 2. FAD get vitamin from Riboflavin (vitamin B2) 3. Co-enzyme A get vitamin from pantothenic acid (vitamin B5) 4. Thiamine pyrophosphate get vitamin from thiamine (vitamin B1)

activation energy

1. Start spontaneous and nonspontaneous reactions 2. Is a barrier or a hill that prevents reactions from occurring 3. Molecules acquire activation energy from the surrounding (environment) or collisions with other molecule inside the cell 4. Is always positive

Explain what an equilibrium constant tells you about a reaction

1. The equilibrium constant is directly proportional to standard free energy change change (See notes) 2. indicates the strength of molecular interactions 3. measures of the binding strength of a covalent interactions between two molecules. The binding strength is important because it also indicates how specific the interaction is between the two molecules. The larger the value of K, the stronger the binding between A and B. • K becomes larger as the binding energy= energy released in the binding interaction--- increases. The larger K is, the greater is the drop in free energy between the dissociated and associated states, and the more tightly the two molecules will bind. • Change of a few non-covalent bonds can have dramatic effect on the binding interactions. EX: eliminating a few hydrogen bonds from a binding interaction can be seen to cause a dramatic decrease in the amount of complex that exists at equilibrium • Small changes in the number of weak bonds can have drastic effects on binding interaction

• Enzymatic Kinetics

1. The study of the factors that influence enzyme activity= is the study of how fast enzymes operates, handle its substrates, how its activity is controlled. • Enzymatic kinetics makes it possible to predict how an individual catalyst will perform and how it will interact with other enzymes in a network.

membrane Protein

1. They are used for many functions by the cell 2. Transport (import and export) particular nutrients, metabolic, and ions in and outside of the cell through the lipid bilayers 3. Anchor/attach membrane to macromolecules on either side (inside or outside of the cell) 4. Are receptors that detect chemical signals in the cell's environment and relay them to the cell interior 5. Enzymes to catalyze reactions (formation or breakage of covalent bonds)

There are two types of opposing streams of chemical reactions in the metabolism of a cell:

1. catabolic pathways 2. anabolic pathways

Above the optimal range

1. enzyme shape is change so much that it cannot form a complex with a substrate. 2. The substrate molecule have too much energy to form a complex. 3. Activity drop to zero and cannot be restored with cooling This happens because the protein is denatured= at a very high temperature the atoms that make up the molecule have so much energy that their violent motion rips the protein molecule apart. Cooling will not return the molecule to its original shape.

What is energetically unfavorable reactions/ non-spontaneous reactions

1. have positive free energy change 2. order 3. G of product is bigger than G of reactant EX: two amino acids are joined together to form a peptide bond (endogenic reactions) Is endogenic and is not favored by enzymes. Can take place only if they are coupled to a second reaction with a negative free energy change so large that the net free energy change of the entire process is negative. Life is possible because enzyme can couple spontaneous reactions with non-spontaneous reactions. G of product is greater than G of reactant. Endogonic reaction

active site

1. is 3-D 2. as a very specific shape and will form a complex with only the substrate that fits in the shape. Substrates that cannot fit in this shape cannot fit into the active site and cannot form a complex with the enzyme. This makes enzymes to catalyze only one reaction or group of reactions with similar substrates. Anything that alters the shape of the active site will affect the enzyme's ability to bind with the substrates and catalyze a reaction.

Describe Km

1. is the affinity of the enzyme for the substrate 2. measure the concentration of substrates needed to make enzymes work efficiently. 3. Is the concentration of substrate at which the enzyme works at half its maximum speed (0.5Vmax). 4. Is the point at which amount of substrate makes the enzyme work at half the Vmax. Low value of Km indicates that a substrate binds very tightly to the enzyme (need few substrates to reach half of Vmax) Large value of Km indicates that enzyme hold weakly to the substrate.( need more substrates to reach half of Vmax)

What enzymes do?

1. lower the activation energy 2. like cells obey the second law of thermodynamics 3. Speed/catalyze up energetically favorable/spontaneous chemical reactions 4. They do not speed up non-spontaneous reactions. They couple them reactions with spontaneous reactions to make them energetically favorable 4. As catalyst, they control the metabolic pathways of the cell 5. Enzymes allow reactions that would not normally occur to proceed rapidly at normal temperature. (thermodynamically unfavorable reactions to proceed) Without enzymes live could not exist. 6.• Enzymes participate in biochemical reactions but do not get consumed by them 7 • Enzymes convert substrates (reactants) to products while remaining unchanged themselves. 8. Lowers the forward and reverse When an enzyme lower the activation energy by the same amount and the equilibrium point and standard free energy remains unchanged

What is standard free energy?

1. makes it possible to compare the energetics of different reactions 2. independent of concentration; it depends only on the intrinsic characters of the reacting molecules, based on their behavior under ideal condition where the concentration of all the reactants are set to the same fixed value of 1 mole/liter. (see notes)

What is energetically favorable reactions/spontaneous reactions

1. reactions that produce disorder by decreasing the energy of the system they belong 2.the free energy change is negative 3. Spontaneous 4. exergonic reactions. Occurs when G of product is less than G of reactant. Free-energy change= Gproduct- Greactant EX: compressed spring relaxes to an expanded state, releasing its stores elastic energy as heat to its surrounding EX: Dissolving salt in water

Regulation of enzyme activity in vivo

1.Synthesize only when needed 2. Synthesized as inactive pro-enzyme 3. Covalent modification by phosphate groups 4. Allosteric regulation by effector molecules Allosteric inhibitors Allosteric activators

unsaturated

A Fatty acid tail with double bond and no maximum number of hydrogen bonds is unsaturated and can break easily at higher temperature. The double bond creates a kink in the hydrogen carbon tail that makes it more difficult for the tail to pack against one another and are more fluid. EX: vegetable oil is liquid at room temperature because it has double bonds and have less hydrogen unsaturated. Cholesterol make up 20% of animal cell membrane. They are shorter and rigid and less permeable

Plasma Membrane

Act as a selective barriers. It separates a cell from the outside environment and I the only membrane in prokaryotic and eukaryotic bacteria. It is involved in cell communication

How are membrane proteins associated with the lipid Bilayers?

All have unique orientation in lipid bilayers which is important for their function depending on how they were synthesized. They are built to be in an environment that is partly aqueous and partly fatty. 1. Many membrane proteins extend through the bilayer with part of their mass on either side. Transmembrane proteins= Their hydrophobic regions lie in the interior of the bilayer and their hydrophilic regions are exposed to the aqueous environment on either side of the membrane. 2. Monolayer Associated= are located in the cytosol associated with the inner leaflet of the lipid bilayer by amphipathic helix on the surface of protein 3. Lipid-Linked= lie entirely outside of bilayer (on one side or the other) and are attached to the membrane only by one or more covalently attached lipid groups 4. Protein-Attached = are bound indirectly to one or the other face of the membrane, help in place only by their interactions with other membrane proteins All this proteins above can be removed by disrupting the lipid bilayers with detergents (which denatures it). Proteins that can be removed from the lipid bilayers are called integral membrane proteins and peripheral membrane proteins

Repulsion between the adjacent negatively charged phosphate groups

All the three groups of phosphate have at least one negative charge due to their ionization at the near neutral PH=7 of the cell. The negative charges repel one another and prevents the covalent bond from linking the phosphate groups together

The catalytic activities of enzymes are often regulated by other molecules

Allosteric inhibition is the mechanism behind feedback inhibition.

formation of mouse-human hybrid cells shows

Because a membrane is two-dimensional fluid, many of its protein can move freely within the plane of the lipid bilayer. this diffusion is show by fusing a mouse with a human cell. that plasma membrane proteins can move laterally in the lipid bilayer.

Enzyme concentration

Because of the ability of enzymes to work over and over again, the rate at which a reaction occurs depends on the amount of enzymes. The amount of enzymes= the amount of substrates that can form an enzyme-substrates complex. 1. Doubling the amount of enzyme doubles the rate of reaction and double Vmax etc.

Why a constant input of energy is needed to sustain living organisms?

Because of the maintenance of order within the cell, cells require a continuous input of energy because when there is no input in energy cells are dead. Cells avoid have chemical reactions at equilibrium because they will die and life will not be possible.

What's one good reason for taking your flintstones?

Because vitamine and minerals are needed for many enzyme

Allosteric Inhibitor

Binding of effector in inhibitor site prevents substrate binding

B-barrel

Can form a channel in a membrane. The amino acid side chains that face the inside of the barrel and the aqueous channel are hydrophilic and on the outside of the barrel are hydrophobic (see PowerPoint)

What is an exergonic reaction

Catabolic reactions are considered to be exergonic, because this process releases the energy stored in energy-yielding molecules. Catabolic breaks down food molecules into small molecules. This generates energy stored in chemical bonds. The chemical bonds release heat. This process requires energy because things are being broken EX: Consider cellular respiration This is a catabolic process in which the energy stored in glucose is released, and used to generate ATP. This is done by taking nutrients from the environment breaking them down to form ATP in mitochondria.

Why cells favor non-spontaneous reactions

Cells favor non-spontaneous reactions to occur in order to grow and divide because they must build highly ordered and energy-rich molecules from small and simple ones—a process that requires an input of energy (endogonic reaction).

Non-completive inhibition

Change the shape of enzymes so that it cannot bind to substrates. non-substrate molecules that bind with part of the enzyme other than the active site and inactive the enzyme. They change the shape of the active site so that substrates do not bind to it.

• Free-energy change apply to

Chemical reactions where covalent bonds are being broken and formed. Interactions where molecules bind to non-covalent bonds Non-covalent interactions are important to the cells because they include the binding of 1. Substrates (reactants) to enzymes 2. Gene regulatory proteins to DNA 3. Protein to another ligand to make functional protein complexes that constitute a living cell. Two molecule (Y and X) will bind to each other if the standard free energy change of the interactions is negative.

Most of the functions cell perform are done by

Chemical reactions. Outside of the cell, chemical reactions occur very slowly to support life when enzymes are not used. In living cells chemical reactions have to be fast in order for life to occur. Enzymes are proteins that catalyze the reactions without being consumed.

Some enzymes require what to be activated?

Co-factors Co-factors are non-protein part of the enzyme. Their primary function is to assist enzyme activity. They help enzymes catalyze reactions. They are embedded in a protein when it is synthesized and stay in the active site. enzymes perform certain reactions that they cannot perform alone. They can be: 1. Metals (magnesium, zinc, copper etc..) 2. co-enzymes (organic molecules such as amino acids, sugars) Co-factors are divided into 1. coenzymes (hemoglobin) and prosthetic groups. A holoenzyme refers to a catalytically active enzyme that consists of both apoenzyme (enzyme without its cofactor(s)) and cofactor. If you are lacking certain co-factors certain enzymes will not be activated. coenzymes are the inactivated form of enzymes (do not have non-proteins to help them perform functions that they cannot do with amino acids)

Where does heat released by the cell come from?

Come from chemical bonds. And the energy comes from the environment

What is the principle of the first law of thermodynamics

Energy cannot be created or destroyed; it can only change forms (principle of energy conversation). Ex: as an animal cell breaks down foodstuffs, some of the energy in the chemical bonds in the food molecules (chemical bond energy) is converted into the thermal motion of molecules (heat energy). This conversion of chemical energy into heat energy is essential if the reactions inside the cell are to cause the universe as a whole to become more disordered as required by the second law Total amount of energy in the universe must always be the same EX: energy goes from potential to kinetic energy. Energy goes from high state to law state. For example: Diffusion, high concentration to law concentration

What is the energy required for breaking bonds (covalent and non-covalent bonds)

Energy required to break covalent bonds X-rays, U-V light energy required to break non-covalent bond heat, vibration at high temperature

explain how enzymes increase the rate of biochemical reactions

Enzyme increase the rate of biochemical reactions by lowering the activation energy. It forms a complex with a reactant or substrate. The substrate stick to the enzyme at the active site like lock and key. The enzyme holds the substrate tightly and the activation energy is lowered. Once is lowered, the product is formed and released in the environment. Enzymes can be used over and over again because they are not consumed in the reaction. • According to the second law of thermodynamics, a chemical reaction can proceed only if it results in a net (overall) increase in the disorder of the universe. Disorder increases when useful free-energy is dissipated as heat. • , allowing the enzyme to bind and repeat the reaction

All proteins must bind to particular ligands to carry out their functions.

Enzymes can be grouped into functional classes (each enzyme catalyze only one reaction at a time) 1. Hexokinase adds a phosphate group to D glucose 2. Trombin cuts one type of blood protein between a particular arginine and its adjacent glycine

Be able to explain the importance of the requirements of coupling biochemical reactions

Enzymes do not speed up non-spontaneous reactions because they have more free-energy. However, they can couple them with a highly spontaneous reaction a high negative free-energy to make to make them energetically favorable.

All membrane protein have what which is essential for their function? and explain the example for trans-- membrane protein

Example: In Trans-membrane receptor protein, the part of the protein that receives signals is on the outside of the cell and the part that passes along the signal is on the inside of the cell (cytosol). They are like this based on how they were synthesized. The portion of transmembrane proteins that receive signals and passes signals are connected by a membrane-spanning segments of the polypeptide chain. The membrane-spanning segments run through the hydrophobic environment of the interior of the lipid bilayer because they are composed largely of amino acids with hydrophobic side chains. The side chains are in lipid environment because they do not like water.

What is the difference between free-energy change and standard free-energy change. Why this difference is important when studying biochemical reactions?

Free-energy change indicate the disorder that result in the universe. Standard free-energy change represents the gain or loss of free energy as one mole of reactant is converted to one mole of product under "standard conditions". helps us predict the outcome of the reaction ( will it proceed to the right or to the left? At what point will it stop?). All molecules are presented at a concentration of 1 M and PH of 7.0

Allostery regulation

Have a shape that is totally different from the shape of the enzyme's preferred substrate. Can adopt two or more slightly different conformations, and by a shift from one to another, their activity can be regulated. Enzymes have at least two different binding sites on their surface: 1. The active site that recognizes the substrates (allosteric activator) 2. One or more sites that recognize regulatory molecules (Allosteric inhibitor). The substrates and regulatory sites must communicate in a way that allows the catalytic events at the active site to be influenced by the binding of the regulatory molecule at its separate site.

Why does hydrolysis of ATP yield energy? What is it about the ATP molecule that makes the hydrolysis of its phosphoanhydride bonds so exergonic

Hydrolysis of ATP to ADP and Pi is exergonic because of charge 1. repulsion between the adjacent negatively charged phosphate groups 2. resonance stabilization of both products of hydrolysis 3. increased entropy and solubility.

Why would anyone need to know exactly how tightly a particular enzyme clutches its substrate? Or whether it can process 1000 or 100 substrates molecules every second?

In order to know if substrates can be added or not added to allow enzymes to work at half their Vmax. If we know the amount of substrates that enzymes can hold, we can try to not keep adding substrates when it reaches Vmax.

Second law of thermodynamics

In the universe or in any isolated system ( matter that is completely isolated from the rest of the universe) the degree of disorder can only increase. The system will change spontaneously toward those arrangements that have the greatest disorder (entropy). System change spontaneously toward arrangements with greater entropy. Spontaneous reactions require more energy The measure of a system's disorder is called entropy of the system. The greater the disorder the greater the entropy Physical and chemical events proceed from a higher energy state to a lower energy state and greater disorder (entropy)

A trans membrane hydrophilic pore can be formed by multiple alpha helices

In this example, five trans membrane alpha helices form water filled channel across the lipid bilayer. The hydrophobic amino acid side chains (green) on one side of each helix contact the hydrophobic hydrocarbon tails, while the hydrophilic side chains (red) on the opposite side of the helices form water-filled pore (see powerpoint)

How cells control the activity of proteins and enzyme

Inside the cell, most proteins and enzymes do not work continuous at full speed. Their activities are regulated in a coordinated fashion so that the cell can maintain itself in an optimal state Cells control 1. How many molecules of each enzyme it makes by regulating the expression of the gene that encodes that protein 2. Confine sets of enzymes to a particular subcellular compartment

Plasma membrane

Is a thin fatty container that held a living cell. Act as a selective barrier that separate and protects the chemical components inside from the outside environment. It does not allow the content inside of the cell to mix with the one outside of the cell. Without the membrane there would be no life and no cell. For cell to survive, it allows nutrients to go inside of the cell and waste products to go outside of the cell by using membrane transport proteins (transporters (passive and active transport proteins and ion channels) (The intracellular membrane enclose the organells and the external plasma membrane is enclose the whole cell)

Why sugars are located only on the extracellular side of the membrane and not on the cytoplasmic side?

Many lipids and proteins have sugars covalently attached to them. The majority of protein have shart chains of sugars (oligosaccharides)linked to them. (protein +oligosaccharides = glycoproteins Others have polysaccharide attached to them = proteoglycans. All the sugars are found on the non-cytosolic side where it forms carbohydrate layer. The carbohydrate protect the cell from mechanical and chemical damage. When oligosaccharides and polysaccharides in the carbohydrate layer absorb water, they give a cell a slimy surface that help the motils cells such as white blood cells to squeeze through narrow spaces, and it prevents blood cells from sticking to one another or to the walls of the blood cells.

The binding of a protein to another molecule is highly selective

Many weak bonds are needed to enable a protein to bind tightly to a second molecule (a ligand). The ligand must precisely fit into the protein's binding site, like a hand and glove, so that a large number of non-covalent bonds can be formed between the protein and the ligand.

Explain and interpret Michaelis-Menten and Lineweaver-Burk plots showing enzymatic activity. This includes determing Vmax and Km values from the graphs

Michaelis-Menten= Inhibitors Lineweaver Burk plots= Increasing the substrate concentration

How salt concentration and PH of the surrounding water alter the active site?

PH is a measure of hydrogen ion (H+) concentration. A high PH means a low (H)+ concentration (basic) and a low PH mean a high (H+) concentration (acid). Within a certain PH range enzyme activity is highest because the enzyme is in its optimum shape. If the optimum range is change a little, It reduces the enzyme activity slightly and substrates can still stick to it. when the optimum range is changed a lot, the shape of enzyme is changed a lot and cannot form a complex with a substrate. This makes the enzyme activity close to zero. Salts and hydrogen ions affect the shape of proteins by interfering with the hydrogen and ionic bonds that hold the protein in its particular shape

How proteins Work to carry out their functions

Proteins do their job by binding to other proteins or small molecules to perform a specific function depending on their shape. Proteins have different amino acids sequences The amino acids give rise to an enormous variety of different protein shapes that determine the protein function based on its chemical proteins. ALL proteins stick to other molecules called ligand to carry out their function depending on their shape. The function/activity/biological properties of proteins depends on their ability to bind specifically to other molecules (ligand), allowing them to act as catalysts (enzyme), structural supports, signal receptors, and tiny motors. • EX: Antibodies (defense protein) attach to viruses or bacteria as part of the body's defenses • Enzyme hexokinase binds glucose and ATP to catalyze a reaction between them • Actin molecules bind to each other to assemble into long filaments

• Metabolic maps:

Suggest which pathways a cell might follow as it converts from nutrients into small molecules, chemical energy, and the larger building blocks of life. Metabolic maps do not reveal how a cell will behave under a particular set condition: which pathways it will take when it is starving, when it is well fed, when oxygen is scarce, when it is stressed and it decides to divide.

The binding between proteins

The binding between proteins and other molecules can be weak or tight. The affinity of enzyme to its substrates is determined by Km. The lower the Km, the tighter the binding 9longer lived) and the higher the Km the weaker the binding= short lived. Any substance that is bound by a protein whether is an ion, small molecules, or large macromolecule is called a ligand for that protein. • The ability for proteins to bind selectively and with high affinity to a ligand is due to the formation of a set of weak, noncovalent bonds—hydrogen bonds, electrostatic attractions, and van der Waals attractions and favorable hydrophobic interactions (spontaneous reactions). The bonds are weak so that many weak bonds can be easily formed. .

EX of a barrel

The example of barrel is found in porin proteins barrels can form only wide channels because there is a limit to how tighly the beta-sheet can be curved to form the barrel. This makes it less versatile than a collection of alpha helices

Explain how protein are separated from all other proteins so that they can be studied

The first step: Solubilize the membrane with detergents that destroy the lipid bilayer by disrupting hydrophobic association.

Why is the Lipid Bilayer a Two dimensional fluid?

The lipid bilayer behaves as a two dimensional fluid because the aqueous environment inside and outside of the cell prevents membrane lipids from escaping from the bilayer, but nothing stops the molecules from moving and changing places with one another within the bilayers. • The two dimension fluid are important for the membrane function and integrity. They are flexible/ can bend • Synthetic lipid such as liposome can be used to study the fluidity of lipid bilayers. They allow biologists to see how small hydrophobic molecule such (carbon dioxide and benzene flow rapidly through the bilayer and how small uncharged polar amino acids, nucleotides, sugars, DNA, RNA, and proteins flow slower through the membrane =hydrophilic).

Lysozyme illustrates how an Enzyme works

The reaction catalyzed by lysozyme is a hydrolysis Hydrolysis: The enzyme break glycosidic bond by adding a water molecule to a single bond between two adjacent sugar groups in the polysaccharide chain. This reaction is energetically favored because the free energy is lowered. However, the reaction can sit many years without being hydrolyzed because the activation energy prevents it from occurring. For hydrolysis to occur, water molecules colliding together have to break the glycosidic bonds lining two sugars together into a distorted shape called transition state by using a lot of energy. Enzymes can be used to lower the energy of activation so that water molecules break the glysodic bond

Why are the first and second law of thermodynamics important for biological systems

They are important because they provide a rule that explain that energy in a cell can nerve be or destroyed. It go from one state to another. The living organisms have to be disorder to obey the second law of thermodynamics.

How Membrane proteins can be solubilized in detergents and purified

To understand a protein fully one needs to know its structure in detail. Membrane proteins are built to operate in an environment that is partly aqueous and partly fatty. Taking them out of this environment and purfying them while preserving their essential structure is not easy. Before an individual protein can be studied in detail, it must be separated from all other cells proteins.

How do enzymes do work?

To understand how enzymes do work, we have to know what chemical reactions are. Chemical reactions are the forming or breaking of chemical bonds between two or more atoms or molecules. For the bonds to be broken or form, energy Is required. Activation energy is the boost that molecules need in order to start the reaction. However, molecules cannot go over the activation energy because they have little energy. Chemical reactions can be speed up in two ways: 1. Adding heat increases the energy of the molecules to go up the hill and over the activation energy 2. Use enzymes to lower the activation energy This will give the molecules sufficient energy to initial the chemical reactions by increasing the rate of activation.

describe Vmax

Vmax is a point at which all enzymes molecules are occupied with substrate all the time and additional substrate concentration will not increase the rate of reaction. Vmax can only be increased by doubling or tripling the amount of enzyme. This will create more enzyme that substrates can bind to at the active site.

What is the importance of Vmax and Km in enzyme kinetics

Vmax is the point at which all of the enzymes are occupied with substrates and any additional amount of substrates will not increase Vmax. Vmax can be increase by doubling or tripling the amount of enzyme. Km indicate the amount of substrates that make the enzymes work at half its Vmax. If km is larger, enzymes hold weakly to the substrates and need to add more substrates to make it work at half its Vmax. If km is lower, the enzyme hold the substrates tightly and need few substrates to work at half it Vmax.

What is the energy required for forming bonds

When forming a bond energy is released When breaking a bond energy is absorb(forming a bond)= need more energy

For chemical reactions to occur in a cell

a living organism must have a source of atoms in the form of food molecules and source of energy from nonliving environment. Cells perform chemical reactions at high temperature (why higher temperature) because it helps enzymes to speed up/ catalyze chemical reactions within the cell . The enzyme-catalyzing reactions are connected in series so that the product of one reaction is the starting material for the next reaction. This result in a long linear reaction pathways called metabolic pathways that link to one another to form a complex web of interconnected reactions. Catalysis allow the cell to control the metabolism.

Lysozyme's actve site

a long groove that holds six linked sugars at the same time. As soon as the polysaccharide binds to from a enzyme-subtrate complex, the enzyme cuts the polysaccharide by catalyzing the addition of a water molecule one of its sugar bonds.

Temperature

a measure of the average kinetic energy (energy of random motion=heat) of the enzyme and substrate molecules. Temperature affect: 1. Enzyme 2. Enzyme-substrate complex At any given temperature the enzyme molecules are vibrating, rotating and moving about.

Phosphorylation cycles

allow protein to switch rapidly from one another. The more rapidly the cycle is turning, the faster the concentration of a phosphorylated protein can change . Keeping the cycle turning costs energy because one ATP molecules is hydrolyzed with each turn in the cyle

detergent

are amphipathic lipilike molecules that have both a hydrophilic and a hydrophobic region. Compare to phospholipid, they have only one hydrophobic tail and behave in different ways. Their one tail makes them be shaped like a cone when they are in water and aggregate into micelles rather than bilayers. They separate proteins from most of phospholipids: when they are mixed in great excess with membranes, the hydrophobic ends of detergent molecules bind to the membrane-spanning hydrophobic region of the trans membrane proteins and hydrophobic tail of the molecule destroy the lipid bilayer and separate proteins from most of phospholipids . By using the polyacrylamide-gel electrophoresis, the hydrophilic end of detergent molecule brings the membrane proteins into solution as protein-detergent complezes and solubilize the phospholipids. The protein-detergent complexes can separate from one another and form the lipd detergent complex

• Hydrophobic molecules

are insoluble in water because they have uncharged nonpolar atoms (have equal number of electrons and proteins) and cannot interact with water molecules. Instead the nonpolar atoms use energy form force the water molecules to reorganize into a highly ordered cagelike structure around the hydrophobic molecule

Antibodies

are proteins that bind very tightly to their targets (antigens). They are produced in vertebrates as a defense against infection. Each anitibody molecule is made of two indentical light chains and two identical heavy chains so that the two antigen-binding sites are identical

Allosteric activators

binding of effector in activator site stabilizes substrate binding site and favors substrates binding

Catabolic pathways (catabolism)=

break down foodstuffs into smaller molecules. This allow it to generate both useful energy for the cell and small molecules that the cell needs as building blocks. Requires a lot of energy

What are Competitive inhibitors used for?

can be used to treat patients who have been poisoned by ethylene glysol. The ethylene glycol is not fatally toxic, it by product—oxalic acid—is lethal. To prevent oxalic acid from forming, the patient is given a large does of ethanol. Ethanol competes with the ethylene glycol for binding to alcohol dehydrogenase. As a result, the ethylene glycol is ummetabolized and eliminated from the body. EX: The active site of an enzyme can bind either competitive inhibitor or the substrates, but not both together. The upper plot shows that inhibition by competitive inhibitor can be overcome by Increaing the substrate concentration. The double-reciprocal plot bellow shows that the Vmax of the competitive inhibitor; the y intercepts is identical for both curves.

Proteins

carry out most of the function of the membranes and give different membranes their individual characteristics

For disorder to occur a cell has to

cells in a living organism must carry out a never-ending stream of chemical reaction that break down small organic molecules (amino acids, sugars, nucleotides, proteins, DNA, RNA) to create other small molecules that cell requires, proteins, nucleic acids and other macromolecules every second.

Energy, catalysis and biosynthesis

create and maintain order in a universe that is always moving toward disorder (Second law of thermodynamics).

Be a able to use given equations to determine free-energy change and equilibrium values for biochemical reactions and able to explain what they calculate values tell you about the given reaction

do exercise from the chemistry book ( chapter 16)

Increase entropy and solubility

entropy increases as a phosphate group is removed from ATP and is no longer fixed in position. The conversion of ATP to ADP decreases the energy of ATP by making the overall reaction exergonic. As a result the ADP and phosphate become more soluble because they are more highly hydrated, and the increased interactions with water molecules lead to a decrease in free energy, adding to the exergonic nature of ATP hydrolysis

The ligand and protein have to fit together, if they do not few non-covalent bonds are form

few non-covalent bonds are formed and the two molecules dissociate as rapidly as they come together. This prevents incorrect and unwanted associations from forming between mismatched molecules. When they are matched correctly, more non-covalent bonds are formed and the proper association between protein and ligand occur. This association persist for a long time. EX: for example, macromolecules come together to form ribosome, the region of protein that associates with ligand= binding site= contain cavity in the protein surfaces form by a particular arrangement of amino acids. EX: hydrophobic alpha helix for a membrane-spanning protein allows it to be inserted into the lipid bilayer for a cell membrane EX: Antibodies are defense proteins produced by the immune system to fight foreign molecules in the body. They are Y-shaped and has two identical binding sites for its antigen, one on each arm of the Y. Each antibody binds to a particular target molecule extremely tightly, by inactivating the antigen or destroying it.

Porin proteins

form larger, water filled pores in mitochondrial and bacterial membrane. Mitochondrial and some bacteria are surrounded by a double memebrane and porins allow the passage of nurients and small ions across their outer membranes while preventing the entry of larger molecules such as antiotics ad toxins

lipid bilayers

gives the membrane its basic structure and serves as a permeability barrier to most water-soluble molecules (Uncharged polar Amino acids, nucleotides, sugars, ions, DNA, Proteins, RNA) on either side of the cell.

Why enzymes are highly selective

highly selective because each enzyme speeds up only one reaction out of many possible reaction that its substrate molecules could undergo. It does this because it directs each of the many molecules in the cell along a specific metabolic reaction pathways. • Due to this a cell use different enzymes with unique properties so that it can catalyze the appropriate reaction faster.

feedback inhibition

inhibition of an enzyme by a product of that reaction or a metabolic pathway. Non-competitive molecules regulate the activities of enzymes. They bind to an enzyme at a special regulatory site by altering the rate at which the enzyme converts its substrates to product An enzyme acting early in a reaction pathway is inhibited by a late product of that pathway. This slow down the rate of reaction by preventing real substrates to entering into the reaction Feedback inhibition is a negative regulation ( prevents an enzyme from acting) Positive regulation ( the enzyme's activity is stimulated by the substrate molecule rather than being shot down. It occurs when the product in one branch of the metabolic maze stimulate the activity of an enzyme in other pathway. For example: ADP +pi react to form ATP

competitive inhibitors

interfere with the active site of the enzymes so substrates cannot bind. Are molecules that are not substrates that compete with real substrates to form a complex with the active site. 1. directly blocks substrates binding. 2.They resemble the substrate that form a complex with an enzyme. 3. They resemble the substrates enough to tie up the enzymes but they differ enough in structure to avoid getting converted to product. 4. You can overcome this by adding more substrates so that enzymes can encounter more substrates than an inhibotpr molecules. 5. Do not change the vmax 6. Do not undergo chemical reactions and live the active site after a short time. 7. unable the enzyme to complex with real substrates and catalyze the reaction 8. If the concentration of competitor is increased, It will complex with the enzyme and the rate of reaction will be slower because the enzyme will be prevented to catalyze the reaction. 9. If the substrate concentration is increased, the rate of reaction increases because enzymes can catalyze the reaction.

The first step to understand enzyme performance

involves determining the maximal velocity Vmax for the reaction it catalyzes. • You can do this by measuring in a test tube how rapidly the reaction proceeds in the presence of different concentrations of substrates \The rates increases as the amount of substrates rises until the reaction reaches its Vmax. • The velocity (vmax) of the reaction is measured by monitoring either how quicly the substrate is consumed or how rapidly the product produced. The appearance of product or the disappearance of substrate can be observed directly with a spectrophotometer. This instrument detects the presence of molecules that absorb light at a selected wavelength. EX: NADH absorbs light at 340nm, while it counterpart NAD+ does not. The reaction that generates NADH (by reduing NAD+) can be monitored by following the formation of NADH at 340nm spectrophometrically.

What is the free energy?

is the energy that can be harnessed to do work or drive chemical reactions.This reflect the loss of orderliness in the way the energy and molecules had been stored in the paper or biological molecules. Measures the amount of disorder created in the universe when a reaction takes place.

Metabolism

is the sum total of all the chemical reactions a cell needs to carry out to survive, grow, and reproduce. This is the center of the chemistry of life.

Liid-linked protein

lipid-linked are attached to a membrane lipid by a covalent bond

Why do living cells do not defy the second law of thermodynamics

living cells generate order instead of disorder so that they can survive, grow, and form complex communities because a cell is not an isolated system. They are a open system. It takes energy from the environment in the form of food, inorganic molecules, or photons of light from the sun and then uses this energy to generate order within itself by converting it chemical bonds or building large macromolecules. The chemical bond is converted into heat. The heat disperse into the cells' environment and increase the entropy of the environment. The amount of heat released by a cell must be great enough that the order generated inside the cell is balance with the decrease in order in the environment

How cells obtain energy from the environment to create the order

living cells need to maintain order at biological level so that they can grow, survive, and reproduce. They create order by using cellular mechanism that extract energy from the environment and convert it into chemical bonds. They take energy from the nonliving environment in the form of food, inorganic molecules or photos from sunlight and convert into chemical bonds. The chemical bonds release heat that create disorder and make the cell obey the second law of thermodynamics. Biological disorder is made possible by the release of heat energy from cells.

What is an endogenic reaction and give an example

means to store energy inside energy storing molecules. Energy is taken in and stored. Molecules are synthesized (anabolism reactions). Formations of bonds. (energy is released because molecules are formed). EX: Synthesis of ADP and Pi (phosphate group) is endergonic because ADP and Pi are being put together to form ATP, a energy carrier that gives energy to cell functions. examples are when smaller molecules are bonded together to form a larger molecule. Energy is released because larger molecules are formed and have more energy. Example: Glucose (C6H12O6) has 6 carbon molecules that are bonded together and with hydrogen atoms and oxygen atoms. These bonds contain a lot of energy that is used for cellular respiration. Carbon atom molecules have more energy than molecules that do not have carbon. Carbon atoms are the basis of life. EX: Photosynthesis uses light energy to drive the synthesis of carbohydrates, in which the energy is stored. This is considered to be an endergonic reaction because light energy is absorbed. (meaning energy is released because carbohydrate is formed). And, because it results in the SYNTHESIS of carbohydrates, this illustrates an example of anabolism It should be noted that the energy released from the catabolism of complex molecules can be used to initiate synthesis in anabolic, endergonic reactions. exergonic reactions are ones in which energy is released with the product of a reaction. on the other hand, endergonic reactions are ones in which energy is needed to create a product of a reaction. There are no exact correlation between exergonic/endergonic and anabolism/catabolism.

There are two groups of cofactors

metals and small organic molecules called coenzymes. Coenzymes are small organic molecules usually obtained from vitamins. Prosthetic groups refer to tightly bound coenzymes, (km is low) EX: Hemoglobin while cosubstrates refer to loosely bound coenzymes (km is high) that are released in the same way as substrates and products. Loosely bound coenzymes differ from substrates in that the same coenzymes may be used by different enzymes in order to bring about proper enzyme activity. The confusing thing about coenzymes is that they are considered as substrates and cofactors Enzymes without their necessary cofactors are called are the inactive form of an enzyme. Cofactors with an apoenzyme are called a holoenzyme, which is the active form. Apoenzymes are inactivated until you combine them with a co-factor.

Peripheral membrane proteins attach to a membrane surface via

noncovalent bonds

All membranes are composed

of lipids bilayers (two fatty hydrophobic opposed sheets) and proteins and share common general structure.

The interaction between sites that are located on separate regions of a protein molecule depend

on conformational changes in protein Conformational changes=binding at one of the sites causes a shift in the protein's structure from one folded shape to a slightly different folded shape. The protein's binding sites for ligands will be altered when the protein change shape because protein take conformations with different contours on their surfaces.

Phosphorylation can either

stimulate protein activity or inhibit it depending on the protein involved and the site it is being phosphorylated. The state of phosphorylation of a protein at any given time depends on the relative activities of the protein kinases and phosphates that act on it.