Sunday, November 2, 2008

Review for Test

Friday, Oct. 31- we did the marshmallow exercise for chapter 4 that block c had already done.
Wednesday, Nov 5- will be the unit test on chapters 2, 4, 5, and 8. and the ch. 12 vocabulary is due.
Friday, Nov. 7- the lab is due.

Here's a review for the test this Wednesday.


CHAPTER TWO:

Life Requires About 25 Chemical Elements

Element = A substance that cannot be broken down into other substances by chemical
reactions.
- All matter is made of elements. Biologically important elements include:

C = carbon
O = oxygen make up 96% of living matter
H = hydrogen
N = nitrogen

Trace element = Element required by an organism in extremely minute quantities.
-Though required by organisms in small quantity, they are indispensable for life
- Examples: B, Cr, Co, Cu, F, I, Fe, Mn, Mo, Se, Si, Sn, V and Zn

Atoms Combine by Chemical Bonding to Form Molecules

Atoms with incomplete valence shells tend to fill those shells by interacting with other atoms.
These interactions of electrons among atoms may allow atoms to form chemical bonds.

Structural formula = Formula which represents the atoms and bonding within a molecule
(H-H).

Molecular formula = Formula which indicates the number and type of atoms (H2).

1. Covalent bonds

Covalent bond = Chemical bond between atoms formed by sharing a pair of valence electrons.
-Strong chemical bond
-Example: molecular hydrogen (H2 )

2. Nonpolar and polar covalent bonds

Electronegativity = Atom's ability to attract and hold electrons.
-The more electronegative an atom, the more strongly it attracts shared electrons.

Nonpolar covalent bond = Covalent bond formed by an equal sharing of electrons
between atoms.
-Occurs when electronegativity of both atoms is about the same (CH4 )
-Molecules made of one element usually have nonpolar covalent bonds (
H2, O2, Cl2, N2).

Polar covalent bond = Covalent bond formed by an unequal sharing of electrons
between atoms.
-Occurs when the atoms involved have different electronegativities.
-Shared electrons spend more time around the more electronegative atom.
-In H2O, the oxygen is strongly electronegative, so negatively
charged electrons spend more time around the oxygen than the hydrogens.
This causes the oxygen atom to have a slight negative charge and the hydrogens to have a slight positive charge.

3. Ionic bonds

Ion = Charged atom or group of atoms.

Anion = An atom that has gained one or more electrons from another atom and has become negatively charged; a negatively charged ion.

Cation = An atom that has lost one or more electrons and has become positively charged; a positively charged ion.

Ionic bond = Bond formed between ions by the electrostatic attraction after the
transfer of an electron.
-The atom attracts the electrons because it is more electronegative
-Ionic compounds are called salts (NaCl or table salt).

The difference in electronegativity between interacting atoms determines if electrons are shared equally (nonpolar covalent), shared unequally (polar covalent), gained or lost (ionic bond).

Weak Chemical Bonds Play Important Roles in the Chemistry of Life

Biologically important weak bonds include the following:
-Hydrogen bonds, ionic bonds in aqueous solutions, and other weak forces such as Van der Waals and hydrophobic interactions
-Make chemical signaling possible in living organisms because they are only temporary associations. Signal molecules can briefly and reversibly bind to receptor molecules on a cell, causing a short-lived response.
-Can form between molecules or between different parts of a single large molecule.
-Help stabilize the three-dimensional shape of large molecules (DNA and proteins).

1. Hydrogen bonds

Hydrogen bond =Chemical bonding in which two molecules are linked together by one or more hydrogen atoms.
-Weak attractive force that is easier to break than a covalent bond
-Is a charge attraction between oppositely charged portions of polar
molecules
-Can occur between a hydrogen that has a slight positive charge when
covalently bonded to an atom with high electronegativity (usually O and N)
-Example: NH3 in H2O

2. Van der Waals interactions
Weak interactions that occur between atoms and molecules that are very close together and result from charge asymetry in electron clouds.

CHAPTER 4:

Aside from water, most biologically important molecules are carbon-based (organic).

The structural and functional diversity of organic molecules emerges from the ability of carbon to form large, complex and diverse molecules by bonding to itself and to other elements such as H, O, N, S, and P.

The Importance of Carbon

Organic chemistry = The branch of chemistry that specializes in the study of carbon
compounds.
Organic molecules = Molecules that contain carbon

The carbon atom:
- Usually has an atomic number of 6; therefore, it has 4 valence electrons.
- Usually completes its outer energy shell by sharing valence electrons in four covalent bonds. (Not likely to form ionic bonds.)
-The four major atomic components of organic molecules are:
Hydrogen
Oxygen
Nitrogen
Carbon

Variation in Carbon Skeletons Contributes to the Diversity of Organic Molecules

Covalent bonds link carbon atoms together in long chains that form the skeletal
framework for organic molecules. These carbon skeletons may vary in:
- Length
- Shape (straight chain, branched, ring)
- Number and location of double bonds
- Other elements covalently bonded to available sites

This variation in carbon skeletons contributes to the complexity and diversity of organic molecules.

Hydrocarbons = Molecules containing only carbon and hydrogen
- Are major components of fossil fuels produced from the organic remains of organisms living millions of years ago
- Have a diversity of carbon skeletons which produce molecules of various lengths and shapes.
- Hydrocarbon chains are hydrophobic because the C-C and C-H bonds are nonpolar.

Functional groups also contribute to the molecular diversity of life

Small characteristic groups of atoms (functional groups) are frequently bonded to the carbon skeleton of organic molecules. These functional groups:
- Have specific chemical and physical properties.
- Are the regions of organic molecules which are commonly chemically reactive.
- Behave consistently from one organic molecule to another.

1. The Hydroxyl Group

Hydroxyl group = A functional group that consists of a hydrogen atom bonded to
an oxygen atom, which is bonded to carbon (-OH).
- Makes the molecule to which it is attached water soluble. Polar water molecules are attracted to the polar hydroxyl group which can form hydrogen bonds.
- Organic compounds with hydroxyl groups are called alcohols.
Example: Ethyl alcohol

2. The Carbonyl Group

Carbonyl group = Functional group that consists of a carbon atom double-bonded
to oxygen (-CO).
- Is a polar group. The oxygen can be involved in hydrogen bonding, and molecules with this functional group are water soluble.
- If the carbonyl is at the end off the carbon skeleton, the compound is an
aldehyde.
Example: Glyceraldehyde
- If the carbonyl is at the end of the carbon skeleton, the compound is a
ketone.
Example: Acetone
- The carbonyl group is the functional group found in sugars.
Example: glucose


3. The Carboxyl Group

Carboxyl group = Functional group that consists of a carbon atom which is both
double-bonded to an oxygen and single-bonded to the oxygen of a hydroxyl group
(-COOH).

- Is a polar group and water soluble. This polarity results from the
combined effect of the two electronegative oxygen atoms bonded to the same carbon.
Example: Acetic acid
- Since it donates protons, this group has acidic properties. Compounds with this
functional group are called carboxylic acids.

4. The Amino Group

Amino group = Functional group that consists of a nitrogen atom bonded to two hydrogens and to the carbon skeleton (-NH2).
Is a polar group and soluble in water.
Acts as a weak base. The unshared pair of electrons on the nitrogen can accept a proton, giving the amino group a +1 charge.
- Organic compounds with this function group are called amines.

5. The Phosphate Group

Phosphate group = Functional group which is the dissociated form of phosphoric acid
(H3P04)
- Loss of two protons by dissociation leaves the phosphate group with a negative
charge.
Has acid properties since it loses protons.
Polar group and soluble in water.
Organic phosphates are important in cellular energy storage and transfer.
(Example: ATP.)

6. The Methyl group

Methyl group = Functional group which consists of a single carbon and three attached
hydrogens (CH3-).

- Hydrocarbons would only have methyl groups.
- Fatty acids, oils and waxes would be examples.
- would be nonpolar and hydrophobic molecules.

7. The Sulfhydryl group

Sulfhydryl group = Functional group composed of a sulfur and a hydrogen (-SH).

-helps stabilize the structure of protein with disulfide bridges
-also called thiols

CHAPTER 5:

Most Polymerization Reactions in Living Organisms Are Condensation Reactions.

Polymerization reactions = Chemical reactions that link two or more small
molecules to form larger molecules with repeating structural units.
Condensation reactions = Polymerization reactions during which monomers are
covalently linked, producing net removal of a water molecule for each covalent linkage.
- One monomer loses a hydroxyl (-OH), and the other monomer loses a hydrogen
(-H).
- Process requires energy.
- Process requires biological catalysts or enzymes.

Hydrolysis = a reaction process that breaks covalent bonds between monomers by the addition of water molecules.
- A hydrogen from the water bonds to one monomer, and the hydroxyl bonds to
the adjacent monomer.
- Example: Digestive enzymes catalyze hydrolytic reactions which break apart
large food molecules into monomers that can be absorbed into the bloodstream.

There Are Four Classes of Macromolecules in Living Organisms:
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic acids

Carbohydrates: Fuel and Building Material

Sugars, the smallest carbohydrates, serve as fuel and carbon sources

Carbohydrates = Organic molecules made of sugars and their polymers
- Monomers or building block molecules are simple sugars called
monosaccharides.
- Carbohydrates are classified by the number of simple sugars.

1. Monosaccharides
Monosaccharides = simple sugar in which C, H, and O occur in the ratio of (CH2O)
-glucose is the most common
- Can be produced by photosynthetic organisms from CO2, H20, and
sunlight
- Store energy in their chemical bonds which is harvested by cellular respiration
- Can be incorporated as monomers into disaccharides and polysaccharides

Characteristics of a sugar:
An -OH group is attached to each carbon except one, which is double bonded to
an oxygen (carbonyl)

Aldehyde
Terminal carbon forms a double bond with oxygen.
Example: glucose

Ketone
Carbonyl group is within the carbon skeleton.
Example: fructose

Size of the carbon skeleton varies from three to seven carbons. The most
common monosaccharides are:

Classification Number of Carbons Example

Triose 3 Glyceraldehyde
Pentose 5 Ribose
Hexose 6 Glucose

2. Disaccharides

Disaccharide = a double sugar that consists of two monosaccharides joined by a glycosidic linkage.
Glycosidic linkage = Covalent bond formed by a condensation reaction between two sugar monomers.

Examples of disaccharides include:
Disaccharide Monomers General Comments

Maltose Glucose + Glucose Important in brewing beer
Lactose Glucose + Galactose Present in milk
Sucrose Glucose + Fructose Table sugar; most prevalent
disaccharide

Polysaccharides Have Storage and Structural Roles

Have two important biological functions:
1. Energy storage (starch and glycogen)
2. Structural support (cellulose and chitin)

1. Storage polysaccharides
Cells hydrolyze storage polysaccharides into sugars as needed. Two most common
storage polysaccharides are starch and glycogen.

Starch = Glucose polymer that is a storage polysaccharide in plants.
- Most animals have digestive enzymes to hydrolyze starch.

Glycogen = Glucose polymer that is a storage polysaccharide in animals.
- Stored in the muscle and liver of humans and other vertebrates

2. Structural polysaccharides

Structural polysaccharides include cellulose and chitin.

Cellulose = Linear unbranched polymer of glucose.
- A major structural component of plant cell walls
- Differs from starch (also a glucose polymer) in its glycosidic linkages
-Cellulose reinforces plant cell walls. Hydrogen bonds hold together parallel cellulose molecules in bundles of microfibrils.

Chitin = A structural polysaccharide that is a polymer of an amino sugar.

-Forms exoskeletons of arthropods
-Found as a building material in the cell walls of some fungi

Lipids: Diverse Hydrophobic Molecules

Lipids = Diverse group of organic compounds that are insoluble in water. Important groups are fats, phospholipids, and steroids. Lipids do not form polymers.

Fats store large amounts of energy
Fats are constructed from:
1. Glycerol, a three-carbon alcohol
2. Fatty acid (carboxylic acid)
- Composed of a carboxyl group at one end and an attached hydrocarbon chains ("tail")
- Carboxyl functional group ("head") has properties of an acid.
- Hydrocarbon chain has a long carbon skeleton usually with an even number of
carbon atoms (most have 16 - 18 carbons).
- Nonpolar C-H bonds make the chain hydrophobic and not water soluble.

Triacylglycerol = A fat composed of three fatty acids bonded to one glycerol.
Some characteristics of fat include:
- The source of variation among fat molecules is the fatty acid composition.
- Fatty acids may vary in length.
- Fatty acids may vary in the number and location of carbon-to-carbon double
bonds.

SATURATED FAT UNSATURATED FAT
-No double bonds between -One or more double bonds between
between carbons in fatty acid tail carbons in fatty acid tail

-Carbon skeleton of fatty acid is -Not saturated
bonded to maximum number of
hydrogens (saturated with
hydrogens)

-Usually a solid at room -Usually a liquid at R.T.
temperature

-animal fats -plant fats
e.g., bacon grease, lard and e.g., corn peanut and olive oil
butter

Fat serves many useful functions:
Energy storage. One gram of fat stores twice as much energy as a gram of
polysaccharide.
More compact fuel reservoir than carbohydrate. Animals store more energy
with less weight than plants which use starch, a bulky form of energy storage.
Cushions vital organs in mammals
Insulates against heat loss

Phospholipids

Phospholipids = Compounds with molecular building blocks of glycerol, two fatty
acids, a phosphate group, and usually, an additional small chemical group attached
to the phosphate.

- Differ from fat in that the third carbon of glycerol is joined to a negatively
charged phosphate group
- Show ambivalent behavior toward water. Hydrocarbon tails are hydrophobic
and the head (phosphate group with attachments) is hydrophilic.
- Are major constituents of cell membranes. At the cell surface, phospholipids
form a bilayer held together by hydrophobic interactions among the
hydrocarbon tails.

Steroids

Steroids = Lipids which have four fused carbon rings with various functional groups
attached.

Cholesterol is an important steroid.
- Is the precursor to many other steroids including
vertebrate sex hormones and bile acids.
- Is a common component of animal cell membranes.

Proteins: The Molecular Tools of the Cell

Polypeptide chains = Polymers of amino acids that are arranged in a specific linear sequence and are linked by peptide bonds.

Protein = A macromolecule that consists of one or more polypeptide chains folded and
coiled into specific conformations.
Have important and varied functions in the cell:
1. Structural support
2. Storage (of amino acids)
3. Transport (e.g., hemoglobin)
4. Signaling (chemical messengers e.g., hormones)
5. Cellular response to chemical stimuli (receptor proteins)
6. Movement (contractile proteins)
7. Defense against foreign substances and disease-causing organisms
(antibodies)
8. Catalysis of biochemical reactions (enzymes)

Vary extensively in structure; each type has a unique three-dimensional shape.
Though they vary in structure and function, they are commonly made of only 20 amino
acid monomers.

A polypeptide is a polymer of amino acids connected in a specific sequence

Amino acid = Building block molecule of a protein; most consist of a carbon, which is covalently bonded to a(n):
1. Hydrogen atom.
2. Carboxyl group.
3. Amino group.
4. Variable R group (side chain) specific to each amino acid. Physical and chemical
properties of the side chain determine the uniqueness of each amino acid.

Polypeptide chains are polymers that are formed when amino acid monomers are linked
by peptide bonds.

Peptide bond = Covalent bond formed by a condensation reaction that links the carboxyl
group of one amino acid to the amino group of another.
Polypeptide chains:
- Range in length from a few monomers to more than a thousand.
- Have unique linear sequences of amino acids.

Four Levels of Protein Structure

a. Primary structure
Primary structure = Unique sequence of amino acids in a protein.

- Determined by genes
- Slight change can affect a protein's conformation and function (e.g., sickle-cell
hemoglobin).

b. Secondary structure
Secondary structure = Repeated coiling and folding of polypeptide backbone.

- Contributes to a protein's overall conformation.
- Stabilized by hydrogen bonds between peptide linkages in the protein's
backbone (carbonyl and amino groups).

c. Tertiary structure
Tertiary structure = The three-dimensional shape of a protein. The irregular
contortions of a protein are due to bonding between and among side chains (R
groups) and to interaction between R groups and the aqueous environment.

Types of bonds contributing to tertiary structure are weak interactions and covalent linkage (both may occur in the same protein).
1) Weak interaction
- Hydrogen bonding between polar side chains.
- Ionic bonds between charged side chains.
- Hydrophobic interactions between nonpolar side chains in
protein's interior.
Hydrophobic interactions = the clustering of hydrophobic molecules as a result of their mutual exclusion from water.
2) Covalent linkage
Disulfide bridges form between two cysteine monomers brought together by folding of the protein.

d. Quaternary structure
Quaternary structure = Structure that results from the interactions between and
several polypeptides chains.

- Some globular proteins have subunits that fit tightly together. Example:
Hemoglobin, a globular protein that has four subunits (two a chains and
two (3 chains)

A protein's three-dimensional shape is a consequence of the interactions responsible for secondary and tertiary structure.
- This conformation is influenced by physical and chemical environmental
conditions.
- If a protein's environment is altered, it may become denatured and lose its native
conformation.

Denaturation = A process that alters a protein's native conformation and biological
activity. Proteins can be denatured by:
- Chemical agents that disrupt hydrogen bonds, ionic bonds and disulfide bridges.
- Excessive heat. Increased thermal agitation disrupts weak interactions.

The fact that some denatured proteins return to their native conformation when
environmental conditions return to normal is evidence that a protein's amino acid
sequence (primary structure) determines conformation. It influences where and which
interactions will occur as the molecule arranges into secondary and tertiary structure.

Nucleic Acids: Informational Polymers

Nucleic acids store and transmit hereditary information
Protein conformation is determined by primary structure. Primary structure, is determined by genes; hereditary units that consist of DNA, a type of nucleic acid.

There are two types of nucleic acids.
1. Deoxyribonucleic acid (DNA)
- Contains coded information that programs all cell activity.
- Contains directions for its own replication.
- Is copied and passed from one generation of cells to another.
- In eukaryotic cells, is found in the nucleus.
- Makes up genes that contain instructions for protein synthesis. Genes do not
directly make proteins, but direct the synthesis of mRNA.

2. Ribonucleic acid (RNA)
- Functions in the actual synthesis of proteins coded for by DNA.
- Sites of protein synthesis are on ribosomes in the cytoplasm.

A nucleic acid strand is a polymer of nucleotides
Nucleic acid = Polymer of nucleotides linked together by condensation reactions.
Nucleotide = Building block molecule of a nucleic acid; made of
(1) a five-carbon sugar covalently bonded to
(2) a phosphate group and
(3) a nitrogenous base.

1. Pentose (5-carbon sugar)
There are two pentoses found in nucleic acids: ribose and deoxyribose.

2. Phosphate
The phosphate group is attached to the number 5 carbon of the sugar.

3. Nitrogenous base
There are two families of nitrogenous bases:
Pyrimidine = Nitrogenous base characterized by a six-membered ring made up of
carbon and nitrogen atoms.
- Cytosine. (C)
- Thymine (T); found only in DNA
- Uracil (U); found only in RNA

Purine = Nitrogenous base characterized by a five-membered ring fused to a six
membered ring.
- Adenine (A)
- Guanine (G)

A nucleic-acid polymer or polynucleotise, results from joining nucleotides together
by covalent bonds called phosphodiester linkages. The bond is formed between the
phosphate of one nucleotide and the sugar of the next.
- Results in a backbone with a repeating pattern of
sugar-phosphate-sugar-phosphate.
- Variable nitrogenous bases are attached to the sugar-phosphate backbone ( to carbon 1 of the sugar).
- Each gene contains a unique linear sequence of nitrogenous bases which codes for a unique linear sequence of amino acids in a protein.

Inheritance is based on precise replication of the DNA double helix
In 1953, James Watson and Francis Crick proposed the double helix as the three
dimensional structure of DNA.
- Consists of two nucleotide chains wound in a double helix.
- The two polynucleotide strands of DNA are held together by hydrogen bonds
between the paired nitrogenous bases and by van der Waals attraction between the stacked bases.
- Base-pairing rules are that adenine (A) always pairs with thymine (T); guanine
(G) always pairs with cytosine (C).
- Most DNA molecules are long, containing thousands or millions of base pairs.

CHAPTER EIGHT:


The Chemistry of Life is Organized Into Metabolic Pathways

Metabolism = Totality of an organism's chemical processes

Metabolic reactions are organized into pathways that are orderly series of enzymatically controlled reactions. Metabolic pathways are generally of two types:

Catabolic pathways = Metabolic pathways that release energy by breaking down
complex molecules to simpler compounds (cellular respiration; provides energy for cellular work).
Anabolic pathways = Metabolic pathways that consume energy to build complicated
molecules from simpler ones (photosynthesis; any synthesis of a macromolecule from its monomers).

Metabolic reactions may be coupled, so that energy released from a catabolic reaction can be used to drive an anabolic one.

Organisms Transform Energy

Energy = Capacity to do work

Kinetic energy = Energy in the process of doing work (energy of motion).
- Heat (thermal energy) is kinetic energy expressed in random movement of
molecules.
- Light energy from the sun is kinetic energy which powers photosynthesis.
Potential energy = Energy that matter possesses because of its location or arrangement (energy of position).
- In the earth's gravitational field, an object on a hill or water behind a dam have
potential energy.
- Chemical energy is potential energy stored in molecules because of the
arrangement of nuclei and electrons in its atoms.

Two Laws of Thermodynamics

Thermodynamics = Study of energy transformations

First Law of Thermodynamics = Energy can be transferred and transformed, but it cannot be created or destroyed (energy of the universe is constant).

Second Law of Thermodynamics = Every energy transfer or transformation makes the universe more disordered (every process increases the entropy of the universe).

Entropy = Quantitative measure of disorder (designated by the letter S).

Organisms Live at the Expense of Free Energy

The amount of energy that is available to do work is described by the concept of free energy. Free energy (G) is related to the system's total energy (H) and its entropy (S) in the following way:
where:
G =free energy
H = total energy
T = temperature in √łK
S = entropy

Free energy (G) is the difference between the total energy and the energy not available for doing work (TS).

Significance of free energy:
a. Indicates the maximum amount of a system's energy which is available to
do work.
b. Indicates whether a reaction will occur spontaneously or not.
-A spontaneous reaction is one that will occur without additional energy.
-In a spontaneous process, G or free energy of a system decreases (G<0). style="text-align: center; color: rgb(51, 51, 255);">Free energy and Metabolism

Exergonic reaction = A reaction that proceeds with a net loss of free energy. Are spontaneous reactions.
Endergonic reaction = An energy-requiring reaction that proceeds with a net gain of free
energy; a reaction that absorbs free energy from its surroundings. not spontaneous.


In cellular metabolism, endergonic reactions (require energy) are driven by coupling them to reactions with a greater negative free energy (exergonic). ATP plays a critical role in this energy coupling.

ATP Powers Cellular Work by Coupling Exergonic to Endergonic Reactions

ATP is the immediate source of energy that drives most cellular work.

The structure and hydrolysis of ATP

ATP (adenosine triphosphate) = Nucleotide with unstable phosphate bonds that the
cell hydrolyzes for energy to drive endergonic reactions.
- When the terminal phosphate bond is hydrolyzed, a phosphate group is removed producing ADP (adenosine dihosphate).
The terminal phosphate bonds of ATP are unstable, so:
-The products of the hydrolysis reaction are more stable than the reactant.
-Hydrolysis of the phosphate bonds is thus exergonic as the system shifts to a more stable state.

How ATP Performs Work

Exergonic hydrolysis of ATP is coupled with endergonic processes by transferring a phosphate group to another molecule.
-Phosphate transfer is enzymatically controlled.
-The molecule acquiring the phosphate (phosphorylated or activated intermediate) becomes more reactive.

The regeneration of ATP

ATP is continually regenerated by the cell.
-Process is rapid (107 molecules used and regenerated/sec/cell).
-Reaction is endergonic.
-Energy to drive the endergonic regeneration of ATP comes from the exergonic process of cellular respiration.

Enzymes

Enzymes speed up metabolic reactions by lowering energy barriers
-A chemical reaction will occur spontaneously if it releases free energy (-G), but it may occur too slowly to be effective in living cells.
-Biochemical reactions require enzymes to speed up and control reaction rates.

Catalyst = Chemical agent that accelerates a reaction without being permanently
changed in the process, so it can be used over and over.

Enzymes = Biological catalysts made of protein.

Free energy of activation (activation energy) = Amount of energy that reactant
molecules must absorb to start a reaction (EA).

Exergonic reaction:
1. Reactants must absorb enough energy (EA) to reach the uphill portion of the curve. Usually the absorption of thermal energy from the surroundings is
enough to break chemical bonds.
2 . Reaction occurs and energy is released as new bonds form (downhill portion
of the curve).

The breakdown of biological macromolecules is exergonic. In order to make these molecules reactive when necessary, cells use biological catalysts called enzymes, which:
-Are proteins.
-Lower EA
-Do not change the nature of a reaction (G), but only speed up a reaction that would have occurred anyway.
-Are very selective for which reaction they will catalyze.

Enzymes are Substrate-Specific

Enzymes are specific for a particular substrate, and that specificity depends upon the
enzyme's three-dimensional shape.

Substrate = The substance an enzyme acts on and makes more reactive.
- An enzyme binds to its substrate and catalyzes its conversion to product. The
enzyme is released in original form.
- The substrate binds to the enzyme's active site.

Active site = Restricted region of an enzyme molecule which binds to the substrate.
- Is usually a pocket or groove on the protein's surface.
-Determines enzyme specificity which is based upon a compatible fit between the
shape of an enzyme's active site and the shape of the substrate.
- Changes its shape in response to the substrate.

Induced fit = Change in the shape of an enzyme's active site, which is induced by
the substrate

Steps in the catalytic cycle of enzymes:
1. Substrate binds to the active site forming an enzyme-substrate complex.
Substrate is held in the active site by weak interactions (e.g., hydrogen bonds
and ionic bonds).
2. Induced fit of the active site around the substrate. Side chains of a few amino
acids in the active site catalyze the conversion of substrate to product.
3. Product departs active site and the enzyme emerges in its original form.

A cell's physical and chemical environment affects enzyme activity

Each enzyme has optimal environmental conditions that favor the most active
enzyme conformation.

1. Effects of temperature and pH
Optimal temperature allows the greatest number of molecular collisions
without denaturing the enzyme.
- Enzyme reaction rate increases with increasing temperature. Kinetic
energy of reactant molecules increases with rising temperature,
which increases substrate collisions with active sites.
- Beyond the optimal temperature, reaction rate slows. The enzyme
denatures when increased thermal agitation of molecules disrupts
weak bonds that stabilize the active conformation.
- Optimal temperature range of most human enzymes is 35oC- 40oC.
Optimal pH range for most enzymes is pH 6 - 8.
- Some enzymes operate best at more extremes of pH.
- For example, the digestive enzyme, pepsin, found in the acid
environment of the stomach has an optimal pH of 2.

2. Enzyme inhibitors

Certain chemicals can selectively inhibit enzyme activity
Competitive inhibitors = Chemicals that resemble an enzyme's normal
substrate and compete with it for the active site.
-Block active site from the substrate.
Noncompetitive inhibitors = Enzyme inhibitors that do not enter the
enzyme's active site, but bind to another part of the enzyme molecule.
- Causes enzyme to change its shape so the active site cannot bind
substrate.
- Selective enzyme inhibition is an essential mechanism in the cell for
regulating metabolic reactions.

Metabolic pathways are regulated by controlling enzyme activity.

Metabolic control often depends on allosteric regulation

1. Allosteric regulation
Allosteric site = Specific receptor site on some part of the enzyme
molecule other than the active site.

Allosteric enzymes have two conformations, one catalytically active and the other
inactive.
Binding of an activator to an allosteric site stabilizes the active conformation.
Binding of an inhibitor (noncompetitive inhibitor) to an allosteric site stabilizes the
inactive conformation.

2. Feedback inhibition

Feedback inhibition = Regulation of a metabolic pathway by its end product, which
inhibits an enzyme within the pathway.

Prevents the cell from wasting chemical resources by synthesizing more product than is necessary.

3. Cooperativity

Substrate molecules themselves may enhance enzyme activity.

Cooperativity = The phenomenon where substrate binding to the active site of one subunit induces a conformational change that enhances substrate binding at the active sites of the other subunits.

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